1
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Sukla S, Dhakshinamoorthy DR, Ramesh AV, Lew S, Su M, Seetharaman J. Crystal structure of human Cep57 C-terminal domain reveals the presence of leucine zipper and the potential microtubule binding region. Proteins 2024. [PMID: 38699879 DOI: 10.1002/prot.26698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
Cep57, a vital centrosome-associated protein, recruits essential regulatory enzymes for centriole duplication. Its dysfunction leads to anomalies, including reduced centrioles and mosaic-variegated aneuploidy syndrome. Despite functional investigations, understanding structural aspects and their correlation with functions is partial till date. We present the structure of human Cep57 C-terminal microtubule binding (MT-BD) domain, revealing conserved motifs ensuring functional preservation across evolution. A leucine zipper, with an adjacent possible microtubule-binding region, potentially forms a stabilizing scaffold for microtubule nucleation-accommodating pulling and tension from growing microtubules. This study highlights conserved structural features of Cep57 protein, compares them with other analogous proteins, and explores how protein function is maintained across diverse organisms.
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Affiliation(s)
- Sanskrita Sukla
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Arvind V Ramesh
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Scott Lew
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Min Su
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Jayaraman Seetharaman
- Department of Pharmacology, Addition Science, and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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2
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Ghosh D. Structures and Functions of Human Placental Aromatase and Steroid Sulfatase, Two Key Enzymes in Estrogen Biosynthesis. Steroids 2023; 196:109249. [PMID: 37207843 DOI: 10.1016/j.steroids.2023.109249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/21/2023]
Abstract
Cytochrome P450 aromatase (AROM) and steroid sulfatase (STS) are the two key enzymes for the biosynthesis of estrogens in human, and maintenance of the critical balance between androgens and estrogens. Human AROM, an integral membrane protein of the endoplasmic reticulum, is a member of the cytochrome P450 superfamily. It is the only enzyme to catalyze the conversion of androgens with non-aromatic A-rings to estrogens characterized by the aromatic A-ring. Human STS, also an integral membrane protein of the endoplasmic reticulum, is a Ca2+-dependent enzyme that catalyzes the hydrolysis of sulfate esters of estrone and dehydroepiandrosterone to the unconjugated steroids, the precursors of the most potent forms of estrogens and androgens, namely, 17β-estradiol, 16α,17β-estriol, testosterone and dihydrotestosterone. Expression of these steroidogenic enzymes locally within organs and tissues of the endocrine, reproductive, and central nervous systems is the key for maintaining high levels of the reproductive steroids. The enzymes have been drug targets for the prevention and treatment of diseases associated with steroid hormone excesses, especially in breast, endometrial and prostate malignancies. Both enzymes have been the subjects of vigorous research for the past six decades. In this article, we review the important findings on their structure-function relationships, specifically, the work that began with unravelling of the closely guarded secrets, namely, the 3-D structures, active sites, mechanisms of action, origins of substrate specificity and the basis of membrane integration. Remarkably, these studies were conducted on the enzymes purified in their pristine forms from human placenta, the discarded and their most abundant source. The purification, assay, crystallization, and structure determination methodologies are described. Also reviewed are their functional quaternary organizations, post-translational modifications and the advancements made in the structure-guided inhibitor design efforts. Outstanding questions that still remain open are summarized in closing.
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Affiliation(s)
- Debashis Ghosh
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210.
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3
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Chang TH, Hsieh FL, Gu X, Smallwood PM, Kavran JM, Gabelli SB, Nathans J. Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae. Proc Natl Acad Sci U S A 2023; 120:e2221103120. [PMID: 36996108 PMCID: PMC10083539 DOI: 10.1073/pnas.2221103120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low-molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration-presumably a coiled coil-held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP-i.e., the long dimension of the pore-and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.
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Affiliation(s)
- Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Fu-Lien Hsieh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Xiaowu Gu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Philip M. Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jennifer M. Kavran
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD21205
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4
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Busch MR, Rajendran C, Sterner R. Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli. Biochemistry 2023; 62:863-872. [PMID: 36599150 DOI: 10.1021/acs.biochem.2c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (kcat) and/or the Michaelis constant (KM). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.
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Affiliation(s)
- Markus R Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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5
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Liang Q, Richey ST, Ur SN, Ye Q, Lau RK, Corbett KD. Structure and activity of a bacterial defense-associated 3'-5' exonuclease. Protein Sci 2022; 31:e4374. [PMID: 35762727 DOI: 10.1002/pro.4374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/30/2022] [Accepted: 06/05/2022] [Indexed: 11/10/2022]
Abstract
The widespread CBASS (cyclic oligonucleotide-based anti-phage signaling system) immune systems in bacteria protect their hosts from bacteriophage infection by triggering programmed cell death. CBASS systems all encode a cyclic oligonucleotide synthase related to eukaryotic cGAS but use diverse regulators and effector proteins including nucleases, phospholipases, and membrane-disrupting proteins to effect cell death. Cap18 is a predicted 3'-5' exonuclease associated with hundreds of CBASS systems, whose structure, biochemical activities, and biological roles remain unknown. Here we show that Cap18 is a DEDDh-family exonuclease related to the bacterial exonucleases RNase T and Orn and has nonspecific 3'-5' DNA exonuclease activity. Cap18 is commonly found in CBASS systems with associated CapW or CapH+CapP transcription factors, suggesting that it may coordinate with these proteins to regulate CBASS transcription in response to DNA damage. These data expand the repertoire of enzymatic activities associated with bacterial CBASS systems and provide new insights into the regulation of these important bacterial immune systems.
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Affiliation(s)
- Qishan Liang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Sara T Richey
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Sarah N Ur
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Qiaozhen Ye
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Rebecca K Lau
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Kevin D Corbett
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
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6
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Li B, Jo M, Liu J, Tian J, Canfield R, Bridwell-Rabb J. Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT. Commun Biol 2022; 5:275. [PMID: 35347217 PMCID: PMC8960804 DOI: 10.1038/s42003-022-03226-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H2O2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H2O2-treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H2O2. The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H2O2-consumption assays. Furthermore, an entrance channel for H2O2 was identified and key residues implicated in H2O2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation. The DNA binding and H2O2 sensing mechanisms are revealed for RexT, a transcriptional regulator found in cyanobacteria of the Nostocales order.
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7
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Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS. Structural features of a minimal intact methyltransferase of a type I restriction-modification system. Int J Biol Macromol 2022; 208:381-389. [PMID: 35337914 DOI: 10.1016/j.ijbiomac.2022.03.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M1S1/2)2 structure reveals a symmetric (S1/2)2 assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M1S1/2 MTase dimer indicates a particular state resembling the structure of M2S1 MTases.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 95326 Kulmbach, Germany
| | - Jun-Ha Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Kumoh National Institute of Technology, 61, Daehak-ro, Gumi, Gyeongbuk 39177, Republic of Korea
| | - Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Thi Yen Ly Huynh
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, Hwasun, Jeonnam 58128, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jimin Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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8
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Xu M, Xu Q, Wang M, Qiu S, Xu D, Zhang W, Wang W, He J, Wang Q, Ran T, Sun B. Crystal structures of TTHA1265 and TTHA1264/TTHA1265 complex reveal an intrinsic heterodimeric assembly. Int J Biol Macromol 2022; 207:424-433. [PMID: 35276293 DOI: 10.1016/j.ijbiomac.2022.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/05/2022]
Abstract
Zinc peptidase M16 family members are widely distributed in most prokaryotic and eukaryotic organisms. M16 family has been divided into three subfamilies, M16A, M16B and M16C, based on sequence alignments and subunit connectivity. TTHA1264, an M16B protein found in Thermus thermophiles HB8, possesses an HXXEH motif essential for Zn2+ binding and catalytic activity. TTHA1265 is another member of M16B, which lacks the metal-binding motif but with a conserved active-site R/Y pair commonly found in the C-terminal half of M16 enzymes. Sequence analysis showed that two genes coding for TTHA1264 and TTHA1265 assemble into a single operon in the bacterial genome. Here, we report the crystal structure of TTHA1265 and TTHA1264/TTHA1265 complex from T. thermophilus HB8. Interestingly, when TTHA1264 and TTHA1265 are present alone, TTHA1264 forms a monomer, TTHA1265 forms a homodimer, respectively. However, TTHA264 and TTHA1265 assembled into a heterodimeric complex, indicating that they prefer to form heterodimer. Biochemical data further confirmed the heterodimeric assembly indicating intrinsic heterodimeric assembly of TTHA1264 and TTHA1265. This property of TTHA1264 and TTHA1265 is consistent with the characteristics of the M16B family.
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Affiliation(s)
- Mengxue Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Qin Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Shenshen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Weizhe Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Bo Sun
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
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9
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Kerchner KM, Mou TC, Sun Y, Rusnac DV, Sprang SR, Briknarová K. The structure of the cysteine-rich region from human histone-lysine N-methyltransferase EHMT2 (G9a). JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100050. [PMID: 34278292 PMCID: PMC8261083 DOI: 10.1016/j.yjsbx.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
Euchromatic histone-lysine N-methyltransferase 1 (EHMT1; G9a-like protein; GLP) and euchromatic histone-lysine N-methyltransferase 2 (EHMT2; G9a) are protein lysine methyltransferases that regulate gene expression and are essential for development and the ability of organisms to change and adapt. In addition to ankyrin repeats and the catalytic SET domain, the EHMT proteins contain a unique cysteine-rich region (CRR) that mediates protein-protein interactions and recruitment of the methyltransferases to specific sites in chromatin. We have determined the structure of the CRR from human EHMT2 by X-ray crystallography and show that the CRR adopts an unusual compact fold with four bound zinc atoms. The structure consists of a RING domain preceded by a smaller zinc-binding motif and an N-terminal segment. The smaller zinc-binding motif straddles the N-terminal end of the RING domain, and the N-terminal segment runs in an extended conformation along one side of the structure and interacts with both the smaller zinc-binding motif and the RING domain. The interface between the N-terminal segment and the RING domain includes one of the zinc atoms. The RING domain is partially sequestered within the CRR and unlikely to function as a ubiquitin ligase.
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Affiliation(s)
- Keshia M Kerchner
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Tung-Chung Mou
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Yizhi Sun
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Domniţa-Valeria Rusnac
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Stephen R Sprang
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Klára Briknarová
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
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10
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Phillips RS, Ting SCK, Anderson K. Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid. Biochemistry 2021; 60:1609-1618. [PMID: 33949189 DOI: 10.1021/acs.biochem.1c00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
d-Glucosaminate-6-phosphate ammonia-lyase (DGL) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that produces 2-keto-3-deoxygluconate 6-phosphate (KDG-6-P) in the metabolism of d-glucosaminic acid by Salmonella enterica serovar typhimurium. We have determined the crystal structure of DGL by SAD phasing with selenomethionine to a resolution of 2.58 Å. The sequence has very low identity with most other members of the aminotransferase (AT) superfamily. The structure forms an octameric assembly as a tetramer of dimers that has not been observed previously in the AT superfamily. PLP is covalently bound as a Schiff base to Lys-213 in the catalytic dimer at the interface of two monomers. The structure lacks the conserved arginine that binds the α-carboxylate of the substrate in most members of the AT superfamily. However, there is a cluster of arginines in the small domain that likely serves as a binding site for the phosphate of the substrate. The deamination reaction performed in D2O gives a KDG-6-P product stereospecifically deuterated at C3; thus, the mechanism must involve an enamine intermediate that is protonated by the enzyme before product release. Nuclear magnetic resonance (NMR) analysis demonstrates that the deuterium is located in the pro-R position in the product, showing that the elimination of water takes place with inversion of configuration at C3, which is unprecedented for a PLP-dependent dehydratase/deaminase. On the basis of the crystal structure and the NMR data, a reaction mechanism for DGL is proposed.
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Affiliation(s)
- Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Samuel C-K Ting
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Kaitlin Anderson
- Department of Genetics, University of Georgia, Athens, Georgia 30602, United States
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11
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Hu X, Kim JK, Yu C, Jun HI, Liu J, Sankaran B, Huang L, Qiao F. Quality-Control Mechanism for Telomerase RNA Folding in the Cell. Cell Rep 2020; 33:108568. [PMID: 33378677 DOI: 10.1016/j.celrep.2020.108568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/12/2020] [Accepted: 12/07/2020] [Indexed: 01/28/2023] Open
Abstract
Long non-coding RNAs can often fold into different conformations. Telomerase RNA, an essential component of the telomerase ribonucleoprotein (RNP) enzyme, must fold into a defined structure to fulfill its function with the protein catalytic subunit (TERT) and other accessory factors. However, the mechanism by which the correct folding of telomerase RNA is warranted in a cell is still unknown. Here we show that La-related protein Pof8 specifically recognizes the conserved pseudoknot region of telomerase RNA and instructs the binding of the Lsm2-8 complex to its mature 3' end, thus selectively protecting the correctly folded RNA from exonucleolytic degradation. In the absence of Pof8, TERT assembles with misfolded RNA and produces little telomerase activity. Therefore, Pof8 plays a key role in telomerase RNA folding quality control, ensuring that TERT only assembles with functional telomerase RNA to form active telomerase. Our finding reveals a mechanism for non-coding RNA folding quality control.
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Affiliation(s)
- Xichan Hu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Jin-Kwang Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697-4560, USA
| | - Hyun-Ik Jun
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Jinqiang Liu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697-4560, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA.
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12
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Sarmiento-Pavía PD, Rodríguez-Hernández A, Rodríguez-Romero A, Sosa-Torres ME. The structure of a novel membrane-associated 6-phosphogluconate dehydrogenase from Gluconacetobacter diazotrophicus (Gd6PGD) reveals a subfamily of short-chain 6PGDs. FEBS J 2020; 288:1286-1304. [PMID: 32621793 DOI: 10.1111/febs.15472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/11/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022]
Abstract
The enzyme 6-phosphogluconate dehydrogenase catalyzes the conversion of 6-phosphogluconate to ribulose-5-phosphate. It represents an important reaction in the oxidative pentose phosphate pathway, producing a ribose precursor essential for nucleotide and nucleic acid synthesis. We succeeded, for the first time, to determine the three-dimensional structure of this enzyme from an acetic acid bacterium, Gluconacetobacter diazotrophicus (Gd6PGD). Active Gd6PGD, a homodimer (70 kDa), was present in both the soluble and the membrane fractions of the nitrogen-fixing microorganism. The Gd6PGD belongs to the newly described subfamily of short-chain (333 AA) 6PGDs, compared to the long-chain subfamily (480 AA; e.g., Ovis aries, Homo sapiens). The shorter amino acid sequence in Gd6PGD induces the exposition of hydrophobic residues in the C-terminal domain. This distinct structural feature is key for the protein to associate with the membrane. Furthermore, in terms of function, the short-chain 6PGD seems to prefer NAD+ over NADP+ , delivering NADH to the membrane-bound NADH dehydrogenase of the microorganisms required by the terminal oxidases to reduce dioxygen to water for energy conservation. ENZYME: ECnonbreakingspace1.1.1.343. DATABASE: Structural data are available in PDB database under the accession number 6VPB.
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13
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Zhu K, Chen H, Jin J, Wang N, Ma G, Huang J, Feng Y, Xin J, Zhang H, Liu H. Functional Identification and Structural Analysis of a New Lipoate Protein Ligase in Mycoplasma hyopneumoniae. Front Cell Infect Microbiol 2020; 10:156. [PMID: 32373550 PMCID: PMC7186572 DOI: 10.3389/fcimb.2020.00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
Mycoplasma hyopneumoniae (M. hyopneumoniae) is the causative agent of pandemic pneumonia among pigs, namely, swine enzootic pneumonia. Although M. hyopneumoniae was first identified in 1965, little is known regarding its metabolic pathways, which might play a pivotal role during disease pathogenesis. Lipoate is an essential cofactor for enzymes important for central metabolism. However, the lipoate metabolism pathway in M. hyopneumoniae is definitely unclear. Here, we identified a novel gene, lpl, encoding a lipoate protein ligase in the genome of M. hyopneumoniae (Mhp-Lpl). This gene contains 1,032 base pairs and encodes a protein of 343 amino acids, which is between 7.5 and 36.09% identical to lipoate protein ligases (Lpls) of other species. Similar to its homologs in other species, Mhp-Lpl catalyzes the ATP-dependent activation of lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of M. hyopneumoniae GcvH (Mhp H) in vitro. Enzymatic and mutagenesis analysis indicate that residue K56 within the SKT sequence of Mhp H protein is the lipoyl moiety acceptor site. The three-dimensional structure showed typical lipoate protein ligase folding, with a large N-terminal domain and a small C-terminal domain. The large N-terminal domain is responsible for the full enzymatic activity of Mhp-Lpl. The identification and characterization of Mhp-Lpl will be beneficial to our understanding of M. hyopneumoniae metabolism. Summary Lipoic acid is an essential cofactor for the activation of some enzyme complexes involved in key metabolic processes. Lipoate protein ligases (Lpls) are responsible for the metabolism of lipoic acid. To date, little is known regarding the Lpls in M. hyopneumoniae. In this study, we identified a lipoate protein ligase of M. hyopneumoniae. We further analyzed the function, overall structure and ligand-binding site of this protein. The lipoate acceptor site on M. hyopneumoniae GcvH was also identified. Together, these findings reveal that Lpl exists in M. hyopneumoniae and will provide a basis for further exploration of the pathway of lipoic acid metabolism in M. hyopneumoniae.
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Affiliation(s)
- Kemeng Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huan Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jin Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ning Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Jiandong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Youjun Feng
- Department of Pathogen Biology and Microbiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiuqing Xin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Henggui Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
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14
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Park JS, Lee JY, Nguyen YTK, Kang NW, Oh EK, Jang DM, Kim HJ, Kim DD, Han BW. Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway. Biomolecules 2020; 10:biom10010163. [PMID: 31968674 PMCID: PMC7022378 DOI: 10.3390/biom10010163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
The N-degron pathway is a proteolytic system in which a single N-terminal amino acid acts as a determinant of protein degradation. Especially, degradation signaling of N-terminal asparagine (Nt-Asn) in eukaryotes is initiated from its deamidation by N-terminal asparagine amidohydrolase 1 (NTAN1) into aspartate. Here, we have elucidated structural principles of deamidation by human NTAN1. NTAN1 adopts the characteristic scaffold of CNF1/YfiH-like cysteine hydrolases that features an α-β-β sandwich structure and a catalytic triad comprising Cys, His, and Ser. In vitro deamidation assays using model peptide substrates with varying lengths and sequences showed that NTAN1 prefers hydrophobic residues at the second-position. The structures of NTAN1-peptide complexes further revealed that the recognition of Nt-Asn is sufficiently organized to produce high specificity, and the side chain of the second-position residue is accommodated in a hydrophobic pocket adjacent to the active site of NTAN1. Collectively, our structural and biochemical analyses of the substrate specificity of NTAN1 contribute to understanding the structural basis of all three amidases in the eukaryotic N-degron pathway.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Jae-Young Lee
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea;
| | - Yen Thi Kim Nguyen
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Nae-Won Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Eun Kyung Oh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea;
| | - Dae-Duk Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
- Correspondence: ; Tel.: +82-2-880-7899
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15
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Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity. Mol Cell 2020; 77:723-733.e6. [PMID: 31932164 DOI: 10.1016/j.molcel.2019.12.010] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/04/2019] [Accepted: 12/12/2019] [Indexed: 12/26/2022]
Abstract
Bacteria possess an array of defenses against foreign invaders, including a broadly distributed bacteriophage defense system termed CBASS (cyclic oligonucleotide-based anti-phage signaling system). In CBASS systems, a cGAS/DncV-like nucleotidyltransferase synthesizes cyclic di- or tri-nucleotide second messengers in response to infection, and these molecules activate diverse effectors to mediate bacteriophage immunity via abortive infection. Here, we show that the CBASS effector NucC is related to restriction enzymes but uniquely assembles into a homotrimer. Binding of NucC trimers to a cyclic tri-adenylate second messenger promotes assembly of a NucC homohexamer competent for non-specific double-strand DNA cleavage. In infected cells, NucC activation leads to complete destruction of the bacterial chromosome, causing cell death prior to completion of phage replication. In addition to CBASS systems, we identify NucC homologs in over 30 type III CRISPR/Cas systems, where they likely function as accessory nucleases activated by cyclic oligoadenylate second messengers synthesized by these systems' effector complexes.
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16
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Hwangbo SA, Kim JW, Jung SJ, Jin KS, Lee JO, Kim JS, Park SY. Characterization of a Dimeric Arginase From Zymomonas mobilis ZM4. Front Microbiol 2019; 10:2755. [PMID: 32038508 PMCID: PMC6988801 DOI: 10.3389/fmicb.2019.02755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/12/2019] [Indexed: 12/23/2022] Open
Abstract
Many organisms have genes to protect themselves from toxic conditions such as high ethanol and/or ammonia concentrations. When a high ethanol condition is induced to Zymomonas mobilis ZM4, a representative ethanologenic organism, this bacterium overexpresses several genes to overcome this ethanol stress. Among them, we characterized a gene product annotated as an arginase (zmARG) from Z. mobilis ZM4. Even though all of the arginase-determining sequence motifs are not strictly conserved in zmARG, this enzyme converts L-arginine to urea and L-ornithine in the presence of a divalent manganese ion. The revealed high-resolution crystal structure of zmARG shows that it has a typical globular α/β arginase fold with a protruded C-terminal helix. Two zinc ions reside in the active site, where one metal ion is penta-coordinated and the other has six ligands, discerning this zmARG from the reported arginases with two hexa-liganded metal ions. zmARG forms a dimeric structure in solution as well as in the crystalline state. The dimeric assembly of zmARG is formed mainly by interaction formed between the C-terminal α-helix of one molecule and the α/β hydrolase fold of another molecule. The presented findings demonstrate the first reported dimeric arginase formed by the C-terminal tail and has two metal ions coordinated by different number of ligands.
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Affiliation(s)
- Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea.,Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, South Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Sun-Ju Jung
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
| | - Jie-Oh Lee
- Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, South Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
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17
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Kowiel M, Brzezinski D, Porebski PJ, Shabalin IG, Jaskolski M, Minor W. Automatic recognition of ligands in electron density by machine learning. Bioinformatics 2019; 35:452-461. [PMID: 30016407 DOI: 10.1093/bioinformatics/bty626] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/12/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting. Results Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identification, in some cases doubling the recognition rates, while requiring significantly less time. Our work shows that machine learning can improve the automation of structure modeling and significantly accelerate the drug screening process of macromolecule-ligand complexes. Availability and implementation Code and data are available on GitHub at https://github.com/dabrze/CheckMyBlob. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
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18
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Liepman AH, Vijayalakshmi J, Peisach D, Hulsebus B, Olsen LJ, Saper MA. Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) From Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1229. [PMID: 31681359 PMCID: PMC6797613 DOI: 10.3389/fpls.2019.01229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/04/2019] [Indexed: 05/14/2023]
Abstract
Photorespiration is an energetically costly metabolic pathway for the recycling of phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) to phosphoglycerate. Arabidopsis alanine:glyoxylate aminotransferase 1 (AGT1) is a peroxisomal aminotransferase with a central role in photorespiration. This enzyme catalyzes various aminotransferase reactions, including serine:glyoxylate, alanine:glyoxylate, and asparagine:glyoxylate transaminations. To better understand structural features that govern the specificity of this enzyme, its crystal structures in the native form (2.2-Å resolution) and in the presence of l-serine (2.1-Å resolution) were solved. The structures confirm that this enzyme is dimeric, in agreement with studies of the active enzyme in solution. In the crystal, another dimer related by noncrystallographic symmetry makes close interactions to form a tetramer mediated in part by an extra carboxyl-terminal helix conserved in plant homologs of AGT1. Pyridoxal 5'-phosphate (PLP) is bound at the active site but is not held in place by covalent interactions. Residues Tyr35' and Arg36', entering the active site from the other subunits in the dimer, mediate interactions between AGT and l-serine when used as a substrate. In comparison, AGT1 from humans and AGT1 from Anabaena lack these two residues and instead position a tyrosine ring into the binding site, which accounts for their preference for l-alanine instead of l-serine. The structure also rationalizes the phenotype of the sat mutant, Pro251 to Leu, which likely affects the dimer interface near the catalytic site. This structural model of AGT1 provides valuable new information about this protein that may enable improvements to the efficiency of photorespiration.
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Affiliation(s)
- Aaron H. Liepman
- Biology Department, Eastern Michigan University, Ypsilanti, MI, United States
| | - J. Vijayalakshmi
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Peisach
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
| | - Brian Hulsebus
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
| | - Laura J. Olsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Mark A. Saper
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
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19
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Been KW, Yoon HJ, Jeon ST, Lee HH. Structural characterization of a putative diguanylate cyclase conserved in hyperthermophiles. Biochem Biophys Res Commun 2019; 518:114-119. [PMID: 31420168 DOI: 10.1016/j.bbrc.2019.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
C-di-GMP, bis-(3'-5')-cyclic dimeric guanosine monophosphate, is a key signaling molecule that regulates many important physiological processes in bacteria. C-di-GMP is synthesized by diguanylate cyclase (DGC) containing the homodimeric GGDEF domain. There are many uncharacterized hypothetical proteins annotated as a putative DGC in bacteria including hyperthermophiles; however, their structures still remain unexplored. Here, we solved the crystal structure of the GGDEF-like domain of Tm0107 protein from Thermotoga maritima at a resolution of 2.1 Å, which shares sequence similarities with DGC proteins in other bacteria. Tm0107 consists of an N-terminal coiled-coil and C-terminal GGDEF-like domain. We showed that the GGDEF-like domain of Tm0107 exists as monomer in solution and is structurally similar to other GGDEF domains. Two zinc ions are coordinated at the interface between two Tm0107 monomers. Based on our measurements of the Stokes radii of Tm0107 by analytical gel filtration, we propose a dimer model of Tm0107 containing both the N-terminal coiled coil and C-terminal GGDEF-like domains. Based on the model, Tm0107 forms a homodimer in a manner different compared to other structurally characterized DGC proteins. These results provide useful structural information about putative DGC proteins containing protein sequences similar to that of Tm0107, which is widely conserved in hyperthermophiles.
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Affiliation(s)
- Kyung Wook Been
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Taeg Jeon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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20
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Kim M, Park SH, Park JS, Kim HJ, Han BW. Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24193529. [PMID: 31569543 PMCID: PMC6803910 DOI: 10.3390/molecules24193529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/07/2023]
Abstract
Human endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1) has been suggested to regulate inflammatory responses in endothelial cells by controlling expression of proteins, interleukin-6 and vascular cell adhesion molecule-1, and by preventing apoptosis. To elucidate the structural basis of the EOLA1 function, we determined its crystal structure at 1.71 Å resolution and found that EOLA1 is structurally similar to an activating signal cointegrator-1 homology (ASCH) domain with a characteristic β-barrel fold surrounded by α-helices. Despite its low sequence identity with other ASCH domains, EOLA1 retains a conserved 'GxKxxExR' motif in its cavity structure. The cavity harbors aromatic and polar residues, which are speculated to accommodate nucleotide molecules as do YT521-B homology (YTH) proteins. Additionally, EOLA1 exhibits a positively charged cleft, similar to those observed in YTH proteins and the ASCH protein from Zymomonas mobilis that exerts ribonuclease activity. This implies that the positively charged cleft in EOLA1 could stabilize the binding of RNA molecules. Taken together, we suggest that EOLA1 controls protein expression through RNA binding to play protective roles against endothelial cell injuries resulting from lipopolysaccharide (LPS)-induced inflammation responses.
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Affiliation(s)
- Minju Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Sang Ho Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea.
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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21
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Fang X, Osipiuk J, Chakravarthy S, Yuan M, Menzer WM, Nissen D, Liang P, Raba DA, Tuz K, Howard AJ, Joachimiak A, Minh DDL, Juarez O. Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis. J Biol Chem 2019; 294:13800-13810. [PMID: 31350338 DOI: 10.1074/jbc.ra119.008261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/23/2019] [Indexed: 12/22/2022] Open
Abstract
The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased Km values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the pKa of the catalytic residue (pK ES1) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. We propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.
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Affiliation(s)
- Xuan Fang
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Jerzy Osipiuk
- Center for Structural Genomics of Infectious Diseases (CSGID), Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60637.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439
| | - Srinivas Chakravarthy
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616.,Biophysics Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - William M Menzer
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Devin Nissen
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Pingdong Liang
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Daniel A Raba
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Andrew J Howard
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases (CSGID), Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60637.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Oscar Juarez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
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22
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Rohlfing AE, Eckenroth BE, Forster ER, Kevorkian Y, Donnelly ML, Benito de la Puebla H, Doublié S, Shen A. The CspC pseudoprotease regulates germination of Clostridioides difficile spores in response to multiple environmental signals. PLoS Genet 2019; 15:e1008224. [PMID: 31276487 PMCID: PMC6636752 DOI: 10.1371/journal.pgen.1008224] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/17/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022] Open
Abstract
The gastrointestinal pathogen, Clostridioides difficile, initiates infection when its metabolically dormant spore form germinates in the mammalian gut. While most spore-forming bacteria use transmembrane germinant receptors to sense nutrient germinants, C. difficile is thought to use the soluble pseudoprotease, CspC, to detect bile acid germinants. To gain insight into CspC's unique mechanism of action, we solved its crystal structure. Guided by this structure, we identified CspC mutations that confer either hypo- or hyper-sensitivity to bile acid germinant. Surprisingly, hyper-sensitive CspC variants exhibited bile acid-independent germination as well as increased sensitivity to amino acid and/or calcium co-germinants. Since mutations in specific residues altered CspC's responsiveness to these different signals, CspC plays a critical role in regulating C. difficile spore germination in response to multiple environmental signals. Taken together, these studies implicate CspC as being intimately involved in the detection of distinct classes of co-germinants in addition to bile acids and thus raises the possibility that CspC functions as a signaling node rather than a ligand-binding receptor.
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Affiliation(s)
- Amy E. Rohlfing
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Brian E. Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Emily R. Forster
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Yuzo Kevorkian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - M. Lauren Donnelly
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hector Benito de la Puebla
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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23
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Hohmann U, Hothorn M. Crystal structure of the leucine-rich repeat ectodomain of the plant immune receptor kinase SOBIR1. Acta Crystallogr D Struct Biol 2019; 75:488-497. [PMID: 31063151 PMCID: PMC6503760 DOI: 10.1107/s2059798319005291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/16/2019] [Indexed: 01/17/2023] Open
Abstract
Plant-unique membrane receptor kinases with leucine-rich repeat (LRR) extracellular domains are key regulators of development and immune responses. Here, the 1.55 Å resolution crystal structure of the immune receptor kinase SOBIR1 from Arabidopsis is presented. The ectodomain structure reveals the presence of five LRRs sandwiched between noncanonical capping domains. The disulfide-bond-stabilized N-terminal cap harbours an unusual β-hairpin structure. The C-terminal cap features a highly positively charged linear motif which was found to be largely disordered in this structure. Size-exclusion chromatography and right-angle light-scattering experiments suggest that SOBIR1 is a monomer in solution. The protruding β-hairpin, a set of highly conserved basic residues at the inner surface of the SOBIR LRR domain and the presence of a genetic missense allele in LRR2 together suggest that the SOBIR1 ectodomain may mediate protein-protein interaction in plant immune signalling.
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Affiliation(s)
- Ulrich Hohmann
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
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24
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West AMV, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. A conserved filamentous assembly underlies the structure of the meiotic chromosome axis. eLife 2019; 8:e40372. [PMID: 30657449 PMCID: PMC6349405 DOI: 10.7554/elife.40372] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/18/2019] [Indexed: 11/30/2022] Open
Abstract
The meiotic chromosome axis plays key roles in meiotic chromosome organization and recombination, yet the underlying protein components of this structure are highly diverged. Here, we show that 'axis core proteins' from budding yeast (Red1), mammals (SYCP2/SYCP3), and plants (ASY3/ASY4) are evolutionarily related and play equivalent roles in chromosome axis assembly. We first identify 'closure motifs' in each complex that recruit meiotic HORMADs, the master regulators of meiotic recombination. We next find that axis core proteins form homotetrameric (Red1) or heterotetrameric (SYCP2:SYCP3 and ASY3:ASY4) coiled-coil assemblies that further oligomerize into micron-length filaments. Thus, the meiotic chromosome axis core in fungi, mammals, and plants shares a common molecular architecture, and likely also plays conserved roles in meiotic chromosome axis assembly and recombination control.
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Affiliation(s)
- Alan MV West
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Scott C Rosenberg
- Department of ChemistryUniversity of California, San DiegoLa JollaUnited States
| | - Sarah N Ur
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
| | - Madison K Lehmer
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Qiaozhen Ye
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Götz Hagemann
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
| | - Iracema Caballero
- Crystallographic MethodsInstitute of Molecular Biology of Barcelona (IBMB-CSIC)BarcelonaSpain
| | - Isabel Usón
- Crystallographic MethodsInstitute of Molecular Biology of Barcelona (IBMB-CSIC)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Amy J MacQueen
- Department of Molecular Biology and BiochemistryWesleyan UniversityMiddletownUnited States
| | - Franz Herzog
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
| | - Kevin D Corbett
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
- Department of ChemistryUniversity of California, San DiegoLa JollaUnited States
- Ludwig Institute for Cancer ResearchLa JollaUnited States
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25
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Park JS, Park MC, Lee KY, Goughnour PC, Jeong SJ, Kim HS, Kim HJ, Lee BJ, Kim S, Han BW. Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity. Int J Biol Macromol 2018; 120:835-845. [PMID: 30171954 DOI: 10.1016/j.ijbiomac.2018.08.171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Asparaginyl-tRNA synthetase (NRS) is not only essential in protein translation but also associated with autoimmune diseases. Particularly, patients with antibodies that recognize NRS often develop interstitial lung disease (ILD). However, the underlying mechanism of how NRS is recognized by immune cells and provokes inflammatory responses is not well-understood. Here, we found that the crystal structure of the unique N-terminal extension domain of human NRS (named as UNE-N, where -N denotes NRS) resembles that of the chemotactic N-terminal domain of NRS from a filarial nematode, Brugia malayi, which recruits and activates specific immune cells by interacting with CXC chemokine receptor 1 and 2. UNE-N induced migration of CC chemokine receptor 3 (CCR3)-expressing cells. The chemokine activity of UNE-N was significantly reduced by suppressing CCR3 expression with CCR3-targeting siRNA, and the loop3 region of UNE-N was shown to interact mainly with the extracellular domains of CCR3 in nuclear magnetic resonance perturbation experiments. Based on these results, evolutionarily acquired UNE-N elicits chemokine activities that would promote NRS-CCR3-mediated proinflammatory signaling in ILD.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Min Chul Park
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Young Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Peter C Goughnour
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Jae Jeong
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Therapeutic Target Discovery Branch, Division of Precision Medicine and Cancer Informatics, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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26
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Moussu S, Augustin S, Roman AO, Broyart C, Santiago J. Crystal structures of two tandem malectin-like receptor kinases involved in plant reproduction. Acta Crystallogr D Struct Biol 2018; 74:671-680. [PMID: 29968676 PMCID: PMC6038381 DOI: 10.1107/s205979831800774x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/23/2018] [Indexed: 01/15/2023] Open
Abstract
Complex cell-to-cell communication between the male pollen tube and the female reproductive organs is required for plant fertilization. A family of Catharanthus roseus receptor kinase 1-like (CrRLK1L) membrane receptors has been genetically implicated in this process. Here, crystal structures of the CrRLK1Ls ANXUR1 and ANXUR2 are reported at 1.48 and 1.1 Å resolution, respectively. The structures reveal a novel arrangement of two malectin-like domains connected by a short β-hairpin linker and stabilized by calcium ions. The canonical carbohydrate-interaction surfaces of related animal and bacterial carbohydrate-binding modules are not conserved in plant CrRLK1Ls. In line with this, the binding of chemically diverse oligosaccharides to ANXUR1 and HERCULES1 could not be detected. Instead, CrRLK1Ls have evolved a protein-protein interface between their malectin domains which forms a deep cleft lined by highly conserved aromatic and polar residues. Analysis of the glycosylation patterns of different CrRLK1Ls and their oligomeric states suggests that this cleft could resemble a binding site for a ligand required for receptor activation of CrRLK1Ls.
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Affiliation(s)
- Steven Moussu
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian Augustin
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Andra-Octavia Roman
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Caroline Broyart
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julia Santiago
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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27
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Didychuk AL, Montemayor EJ, Carrocci TJ, DeLaitsch AT, Lucarelli SE, Westler WM, Brow DA, Hoskins AA, Butcher SE. Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities. Nat Commun 2017; 8:497. [PMID: 28887445 PMCID: PMC5591277 DOI: 10.1038/s41467-017-00484-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/02/2017] [Indexed: 01/06/2023] Open
Abstract
U6 small nuclear ribonucleoprotein (snRNP) biogenesis is essential for spliceosome assembly, but not well understood. Here, we report structures of the U6 RNA processing enzyme Usb1 from yeast and a substrate analog bound complex from humans. Unlike the human ortholog, we show that yeast Usb1 has cyclic phosphodiesterase activity that leaves a terminal 3′ phosphate which prevents overprocessing. Usb1 processing of U6 RNA dramatically alters its affinity for cognate RNA-binding proteins. We reconstitute the post-transcriptional assembly of yeast U6 snRNP in vitro, which occurs through a complex series of handoffs involving 10 proteins (Lhp1, Prp24, Usb1 and Lsm2–8) and anti-cooperative interactions between Prp24 and Lhp1. We propose a model for U6 snRNP assembly that explains how evolutionarily divergent and seemingly antagonistic proteins cooperate to protect and chaperone the nascent snRNA during its journey to the spliceosome. The mechanism of U6 small nuclear ribonucleoprotein (snRNP) biogenesis is not well understood. Here the authors characterize the enzymatic activities and structures of yeast and human U6 RNA processing enzyme Usb1, reconstitute post-transcriptional assembly of yeast U6 snRNP in vitro, and propose a model for U6 snRNP assembly.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA.,Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Andrew T DeLaitsch
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Stefani E Lucarelli
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA. .,National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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28
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Simmons CR, Zhang F, MacCulloch T, Fahmi N, Stephanopoulos N, Liu Y, Seeman NC, Yan H. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. J Am Chem Soc 2017; 139:11254-11260. [PMID: 28731332 DOI: 10.1021/jacs.7b06485] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.
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Affiliation(s)
| | | | | | | | | | | | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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29
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Maderbocus R, Fields BL, Hamilton K, Luo S, Tran TH, Dietrich LEP, Tong L. Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer. Nat Commun 2017; 8:160. [PMID: 28757619 PMCID: PMC5534430 DOI: 10.1038/s41467-017-00233-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/12/2017] [Indexed: 11/26/2022] Open
Abstract
Pseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD–MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Here we report the crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer, as well as biochemical and functional studies based on the structural information. We observe a malonate molecule in the active site of MdcA and we also determine the structure of malonate decarboxylase with CoA in the active site of MdcD–MdcE. Both structures provide molecular insights into malonate decarboxylase catalysis. Mutations in the hetero-tetramer interface can abolish holoenzyme formation. Mutations in the hetero-tetramer interface and the active sites can abolish Pseudomonas aeruginosa growth in a defined medium with malonate as the sole carbon source. Some aerobic bacteria contain a biotin-independent malonate decarboxylase (MDC), which allows them to use malonate as the sole carbon source. Here, the authors present the crystal structure of a Pseudomonas MDC and give insights into its catalytic mechanism and function.
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Affiliation(s)
- Riyaz Maderbocus
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Blanche L Fields
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Keith Hamilton
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Shukun Luo
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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30
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Lu G, Xu Y, Zhang K, Xiong Y, Li H, Cui L, Wang X, Lou J, Zhai Y, Sun F, Zhang XC. Crystal structure of E. coli apolipoprotein N-acyl transferase. Nat Commun 2017; 8:15948. [PMID: 28885614 PMCID: PMC5500890 DOI: 10.1038/ncomms15948] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/13/2017] [Indexed: 11/09/2022] Open
Abstract
In Gram-negative bacteria, lipid modification of proteins is catalysed in a three-step pathway. Apolipoprotein N-acyl transferase (Lnt) catalyses the third step in this pathway, whereby it transfers an acyl chain from a phospholipid to the amine group of the N-terminal cysteine residue of the apolipoprotein. Here, we report the 2.6-Å crystal structure of Escherichia coli Lnt. This enzyme contains an exo-membrane nitrilase domain fused to a transmembrane (TM) domain. The TM domain of Lnt contains eight TM helices which form a membrane-embedded cavity with a lateral opening and a periplasmic exit. The nitrilase domain is located on the periplasmic side of the membrane, with its catalytic cavity connected to the periplasmic exit of the TM domain. An amphipathic lid loop from the nitrilase domain interacts with the periplasmic lipid leaflet, forming an interfacial entrance from the lipid bilayer to the catalytic centre for both the lipid donor and acceptor substrates.
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Affiliation(s)
- Guangyuan Lu
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yingzhi Xu
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kai Zhang
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06411, USA
| | - He Li
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Lei Cui
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Xianping Wang
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jizhong Lou
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yujia Zhai
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Fei Sun
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xuejun C Zhang
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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31
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Structural basis of dual Ca 2+/pH regulation of the endolysosomal TRPML1 channel. Nat Struct Mol Biol 2017; 24:205-213. [PMID: 28112729 PMCID: PMC5336481 DOI: 10.1038/nsmb.3362] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/12/2016] [Indexed: 12/01/2022]
Abstract
Organellar ion channels are essential for cell physiology. Their activities are often regulated by Ca2+ and H+, which are concentrated in many organelles. Here we report a novel structural element critical for Ca2+/pH dual regulation of TRPML1, a Ca2+ release channel crucial for endolysosomal functions. TRPML1 mutations cause mucolipidosis type IV (MLIV), a severe lysosomal storage disorder characterized by neurodegeneration, mental retardation and blindness. We obtained high-resolution crystal structures of a 213-amino acid luminal domain of human TRPML1 that harbors three missense MLIV-causing mutations. This domain forms a tetramer with a highly electronegative central pore formed by a novel luminal pore-loop. Cysteine crosslinking and cryo-EM confirm this structure in the full-length channel. Structure-function studies demonstrate that Ca2+ and H+ interact with the luminal pore to exert physiologically important regulation. The MLIV-causing mutations disrupt the luminal domain structure and cause TRPML1 mislocalization. Our study provides a structural underpinning for TRPML1's regulation, assembly and pathogenesis.
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32
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Wild R, Hothorn M. The macro domain as fusion tag for carrier-driven crystallization. Protein Sci 2016; 26:365-374. [PMID: 27774698 DOI: 10.1002/pro.3073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/27/2016] [Accepted: 10/20/2016] [Indexed: 12/16/2022]
Abstract
Obtaining well-ordered crystals remains a significant challenge in protein X-ray crystallography. Carrier-driven crystallization can facilitate crystal formation and structure solution of difficult target proteins. We obtained crystals of the small and highly flexible SPX domain from the yeast vacuolar transporter chaperone 4 (Vtc4) when fused to a C-terminal, non-cleavable macro tag derived from human histone macroH2A1.1. Initial crystals diffracted to 3.3 Å resolution. Reductive protein methylation of the fusion protein yielded a new crystal form diffracting to 2.1 Å. The structures were solved by molecular replacement, using isolated macro domain structures as search models. Our findings suggest that macro domain tags can be employed in recombinant protein expression in E. coli, and in carrier-driven crystallization.
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Affiliation(s)
- Rebekka Wild
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Switzerland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Switzerland
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33
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Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature 2016; 539:43-47. [PMID: 27680699 PMCID: PMC5161637 DOI: 10.1038/nature19825] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 09/07/2016] [Indexed: 11/30/2022]
Abstract
BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally toxic oligomeric pores. The small size of the crystals, 50 unit cells per edge, on average, has impeded structural characterization by conventional means. Here, we report the structure of BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser (XFEL). The structure reveals tyrosine and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.
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Affiliation(s)
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA
| | - Mari Gingery
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Jose A Rodriguez
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Robert H Hice
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA
| | - Nicolas Coquelle
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Hyun-Woo Park
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA
| | - Monarin Uervirojnangkoorn
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Dennis K Bideshi
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA
| | - Axel T Brunger
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Brian A Federici
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - David S Eisenberg
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA
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Simmons CR, Zhang F, Birktoft JJ, Qi X, Han D, Liu Y, Sha R, Abdallah HO, Hernandez C, Ohayon YP, Seeman NC, Yan H. Construction and Structure Determination of a Three-Dimensional DNA Crystal. J Am Chem Soc 2016; 138:10047-54. [PMID: 27447429 DOI: 10.1021/jacs.6b06508] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components.
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Affiliation(s)
| | | | - Jens J Birktoft
- Department of Chemistry, New York University , New York, New York 10003, United States
| | | | | | | | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Carina Hernandez
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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35
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Zhang Q, Harding R, Hou F, Dong A, Walker JR, Bteich J, Tong Y. Structural Basis of the Recruitment of Ubiquitin-specific Protease USP15 by Spliceosome Recycling Factor SART3. J Biol Chem 2016; 291:17283-92. [PMID: 27255711 DOI: 10.1074/jbc.m116.740787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) USP15 and USP4 belong to a subset of USPs featuring an N-terminal tandem domain in USP (DUSP) and ubiquitin-like (UBL) domain. Squamous cell carcinoma antigen recognized by T-cell 3 (SART3), a spliceosome recycling factor, binds to the DUSP-UBL domain of USP15 and USP4, recruiting them to the nucleus from the cytosol to control deubiquitination of histone H2B and spliceosomal proteins, respectively. To provide structural insight, we solved crystal structures of SART3 in the apo-form and in complex with the DUSP-UBL domain of USP15 at 2.0 and 3.0 Å, respectively. Structural analysis reveals SART3 contains 12 half-a-tetratricopeptide (HAT) repeats, organized into two subdomains, HAT-N and HAT-C. SART3 dimerizes through the concave surface of HAT-C, whereas the HAT-C convex surface binds USP15 in a novel bipartite mode. Isothermal titration calorimetry measurements and mutagenesis analysis confirmed key residues of USP15 involved in the interaction and indicated USP15 binds 20-fold stronger than USP4.
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Affiliation(s)
- Qi Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Rachel Harding
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Feng Hou
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Aiping Dong
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - John R Walker
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Joseph Bteich
- the Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, and
| | - Yufeng Tong
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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36
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Filippova EV, Kieser KJ, Luan CH, Wawrzak Z, Kiryukhina O, Rubin EJ, Anderson WF. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. FEBS J 2016; 283:2206-18. [PMID: 27101811 PMCID: PMC5245116 DOI: 10.1111/febs.13738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/30/2016] [Accepted: 04/15/2016] [Indexed: 01/21/2023]
Abstract
UNLABELLED Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic-resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin-binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor-free form and in complex with penicillin V are reported. We used site-directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β-lactams. Structural comparison of the PonA1 apo-form and the antibiotic-bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4'-α3 surrounding the penicillin-binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β-lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall-targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections. DATABASE Structural data are available in the PDB database under the accession numbers 5CRF and 5CXW.
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Affiliation(s)
- Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karen J Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chi-Hao Luan
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Zdzislaw Wawrzak
- Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Evanston, IL, USA
| | - Olga Kiryukhina
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Safarian S, Rajendran C, Müller H, Preu J, Langer JD, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, Michel H. Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Science 2016; 352:583-6. [PMID: 27126043 DOI: 10.1126/science.aaf2477] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/28/2016] [Indexed: 12/29/2022]
Abstract
The cytochrome bd oxidases are terminal oxidases that are present in bacteria and archaea. They reduce molecular oxygen (dioxygen) to water, avoiding the production of reactive oxygen species. In addition to their contribution to the proton motive force, they mediate viability under oxygen-related stress conditions and confer tolerance to nitric oxide, thus contributing to the virulence of pathogenic bacteria. Here we present the atomic structure of the bd oxidase from Geobacillus thermodenitrificans, revealing a pseudosymmetrical subunit fold. The arrangement and order of the heme cofactors support the conclusions from spectroscopic measurements that the cleavage of the dioxygen bond may be mechanistically similar to that in the heme-copper-containing oxidases, even though the structures are completely different.
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Affiliation(s)
- Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
| | - Chitra Rajendran
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. Present address: Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstrasse 31, D-93051 Regensburg, Germany
| | - Hannelore Müller
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
| | - Julia Preu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. Present address: Department of Molecular Membrane Biology, Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, D-60438 Frankfurt/Main, Germany
| | | | - Taichiro Hirose
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Tomoichirou Kusumoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Junshi Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany.
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38
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Jorda J, Sawaya MR, Yeates TO. Progress in low-resolution ab initio phasing with CrowdPhase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:446-53. [PMID: 26960132 PMCID: PMC4784676 DOI: 10.1107/s2059798316003405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 02/26/2016] [Indexed: 11/21/2022]
Abstract
New developments in CrowdPhase, a collaborative online game for tackling the low-resolution phase problem, are presented. The new features address several crystallographic issues and extend the reach of CrowdPhase to a broader range of experimental data sets. Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.
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Affiliation(s)
- Julien Jorda
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
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39
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Kim JY, Nakayama M, Toyota H, Kurisu G, Hase T. Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin. J Biochem 2016; 160:101-9. [DOI: 10.1093/jb/mvw016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/01/2016] [Indexed: 11/14/2022] Open
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40
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Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu Z, Li D, Song H. Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1. Cell Rep 2016; 14:2030-9. [PMID: 26904952 DOI: 10.1016/j.celrep.2016.02.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/20/2016] [Accepted: 02/02/2016] [Indexed: 11/27/2022] Open
Abstract
Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the β hairpin in other SF1B DNA helicases folds into an extended loop followed by an α helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90° at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1.
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Affiliation(s)
- Xianglian Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Wendan Ren
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Yang He
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Chen Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Zhou Liu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Dewang Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Haiwei Song
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.
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An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels. Nat Commun 2016; 7:8770. [PMID: 26753910 PMCID: PMC4730032 DOI: 10.1038/ncomms9770] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/01/2015] [Indexed: 01/07/2023] Open
Abstract
Gap junction channels mediate intercellular signalling that is crucial in tissue development, homeostasis and pathologic states such as cardiac arrhythmias, cancer and trauma. To explore the mechanism by which Ca(2+) blocks intercellular communication during tissue injury, we determined the X-ray crystal structures of the human Cx26 gap junction channel with and without bound Ca(2+). The two structures were nearly identical, ruling out both a large-scale structural change and a local steric constriction of the pore. Ca(2+) coordination sites reside at the interfaces between adjacent subunits, near the entrance to the extracellular gap, where local, side chain conformational rearrangements enable Ca(2+)chelation. Computational analysis revealed that Ca(2+)-binding generates a positive electrostatic barrier that substantially inhibits permeation of cations such as K(+) into the pore. Our results provide structural evidence for a unique mechanism of channel regulation: ionic conduction block via an electrostatic barrier rather than steric occlusion of the channel pore.
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42
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Dauter Z, Wlodawer A. Progress in protein crystallography. Protein Pept Lett 2016; 23:201-10. [PMID: 26732246 PMCID: PMC6287266 DOI: 10.2174/0929866523666160106153524] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/26/2015] [Accepted: 01/03/2016] [Indexed: 11/22/2022]
Abstract
Macromolecular crystallography evolved enormously from the pioneering days, when structures were solved by "wizards" performing all complicated procedures almost by hand. In the current situation crystal structures of large systems can be often solved very effectively by various powerful automatic programs in days or hours, or even minutes. Such progress is to a large extent coupled to the advances in many other fields, such as genetic engineering, computer technology, availability of synchrotron beam lines and many other techniques, creating the highly interdisciplinary science of macromolecular crystallography. Due to this unprecedented success crystallography is often treated as one of the analytical methods and practiced by researchers interested in structures of macromolecules, but not highly competent in the procedures involved in the process of structure determination. One should therefore take into account that the contemporary, highly automatic systems can produce results almost without human intervention, but the resulting structures must be carefully checked and validated before their release into the public domain.
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Affiliation(s)
- Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD and Argonne, IL, USA.
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43
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Schumacher MA, Zeng W, Huang KH, Tchorzewski L, Janakiraman A. Structural and Functional Analyses Reveal Insights into the Molecular Properties of the Escherichia coli Z Ring Stabilizing Protein, ZapC. J Biol Chem 2015; 291:2485-98. [PMID: 26655719 DOI: 10.1074/jbc.m115.697037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli cell division is driven by the tubulin-like GTPase, FtsZ, which forms the cytokinetic Z-ring. The Z-ring serves as a dynamic platform for the assembly of the multiprotein divisome, which catalyzes membrane cleavage to create equal daughter cells. Several proteins effect FtsZ assembly, thereby providing spatiotemporal control over cell division. One important class of FtsZ interacting/regulatory proteins is the Z-ring-associated proteins, Zaps, which typically modulate Z-ring formation by increasing lateral interactions between FtsZ protofilaments. Strikingly, these Zap proteins show no discernable sequence similarity, suggesting that they likely harbor distinct structures and mechanisms. The 19.8-kDa ZapC in particular shows no homology to any known protein. To gain insight into ZapC function, we determined its structure to 2.15 Å and performed genetic and biochemical studies. ZapC is a monomer composed of two domains, an N-terminal α/β region and a C-terminal twisted β barrel-like domain. The structure contains two pockets, one on each domain. The N-domain pocket is lined with residues previously implicated to be important for ZapC function as an FtsZ bundler. The adjacent C-domain pocket contains a hydrophobic center surrounded by conserved basic residues. Mutagenesis analyses indicate that this pocket is critical for FtsZ binding. An extensive FtsZ binding surface is consistent with the fact that, unlike many FtsZ regulators, ZapC binds the large FtsZ globular core rather than C-terminal tail, and the presence of two adjacent pockets suggests possible mechanisms for ZapC-mediated FtsZ bundling.
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Affiliation(s)
- Maria A Schumacher
- From the Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710,
| | - Wenjie Zeng
- From the Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710
| | - Kuo-Hsiang Huang
- Department of Biology, The City College of CUNY, New York, New York 10031, and The Graduate Center of CUNY, New York, New York 10016
| | - Lukasz Tchorzewski
- Department of Biology, The City College of CUNY, New York, New York 10031, and
| | - Anuradha Janakiraman
- Department of Biology, The City College of CUNY, New York, New York 10031, and The Graduate Center of CUNY, New York, New York 10016
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Reardon-Robinson ME, Osipiuk J, Jooya N, Chang C, Joachimiak A, Das A, Ton-That H. A thiol-disulfide oxidoreductase of the Gram-positive pathogen Corynebacterium diphtheriae is essential for viability, pilus assembly, toxin production and virulence. Mol Microbiol 2015; 98:1037-50. [PMID: 26294390 PMCID: PMC4981772 DOI: 10.1111/mmi.13172] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2015] [Indexed: 12/19/2022]
Abstract
The Gram-positive pathogen Corynebacterium diphtheriae exports through the Sec apparatus many extracellular proteins that include the key virulence factors diphtheria toxin and the adhesive pili. How these proteins attain their native conformations after translocation as unfolded precursors remains elusive. The fact that the majority of these exported proteins contain multiple cysteine residues and that several membrane-bound oxidoreductases are encoded in the corynebacterial genome suggests the existence of an oxidative protein-folding pathway in this organism. Here we show that the shaft pilin SpaA harbors a disulfide bond in vivo and alanine substitution of these cysteines abrogates SpaA polymerization and leads to the secretion of degraded SpaA peptides. We then identified a thiol-disulfide oxidoreductase (MdbA), whose structure exhibits a conserved thioredoxin-like domain with a CPHC active site. Remarkably, deletion of mdbA results in a severe temperature-sensitive cell division phenotype. This mutant also fails to assemble pilus structures and is greatly defective in toxin production. Consistent with these defects, the ΔmdbA mutant is attenuated in a guinea pig model of diphtheritic toxemia. Given its diverse cellular functions in cell division, pilus assembly and toxin production, we propose that MdbA is a component of the general oxidative folding machine in C. diphtheriae.
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Affiliation(s)
- Melissa E. Reardon-Robinson
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
- Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
| | - Neda Jooya
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Chungyu Chang
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
- Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
| | - Asis Das
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Hung Ton-That
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
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Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R. The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains. Biochim Biophys Acta Gen Subj 2015; 1860:445-51. [PMID: 26549874 DOI: 10.1016/j.bbagen.2015.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D). METHODS The structural features of RpfB3D have been investigated combining x-ray crystallography and biophysical studies. RESULTS AND CONCLUSIONS The crystal structure of RpfB3D provides the first structural characterization of a DUF348 domain and revealed an unexpected structural relationship with ubiquitin. The crystal structure also provides specific structural features of these domains explaining their frequent association with G5 domains. GENERAL SIGNIFICANCE Results provided novel insights into the mechanism of peptidoglycan degradation necessary to the resuscitation of M. tuberculosis. Features of the DUF348 domain add structural data to a large set of proteins embedding this domain. Based on its structural similarity to ubiquitin and frequent association to the G5 domain, we propose to name this domain as G5-linked-Ubiquitin-like domain, UBLG5.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, SW7 2AZ, UK
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy.
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New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins. Sci Rep 2015; 5:15660. [PMID: 26489670 PMCID: PMC4614863 DOI: 10.1038/srep15660] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/29/2015] [Indexed: 02/08/2023] Open
Abstract
Roquins are a family of highly conserved RNA-binding proteins that also contain a RING-type E3 ubiquitin ligase domain. They repress constitutive decay elements containing mRNAs and play a critical role in RNA homeostasis and immunological self-tolerance. Here we present the crystal structures of the RNA-binding region of Roquin paralog RC3H2 in both apo- and RNA-bound forms. The RNA-binding region has a bipartite architecture composed of ROQ and HEPN domains, and can bind to stem-loop and double-stranded RNAs simultaneously. The two domains undergo a large orientation change to accommodate RNA duplex binding. We profiled E2 ubiquitin-conjugating enzymes that pair with Roquins and found that RC3H1 and RC3H2 interact with two sets of overlapping but not identical E2 enzymes to drive the assembly of polyubiquitin chains of different linkages. Crystal structures, small-angle X-ray scattering, and E2 profiling revealed that while the two paralogs are highly homologous, RC3H2 and RC3H1 are different in their structures and functions. We also demonstrated that RNA duplex binding to RC3H2 cross-talks with its E3 ubiquitin ligase function using an in vitro auto-ubiquitination assay.
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Choi H, Kim HJ, Matsuura A, Mikami B, Yoon HJ, Lee HH. Structural and functional studies of a metallo-β-lactamase unveil a new type of structurally encoded nickel-containing heterodinuclear site. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2054-65. [PMID: 26457429 DOI: 10.1107/s1399004715014807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 08/06/2015] [Indexed: 11/10/2022]
Abstract
The selection of correct metal ions with high fidelity against competing cellular cations is crucial for the function of many metalloenzymes; however, the understanding of the principles that govern metal selectivity is still incomplete. In this study, the crystal structure of the Tm1162 protein from Thermotoga maritima, a metallo-β-lactamase, is reported. Several crystal structures of wild-type Tm1162 and its mutants were solved. Homologues of Tm1162 are widely distributed in bacteria and archaea, including several human pathogens. The monomer possesses an αβ/βα fold, with the core β-strands having the β-sheet sandwich structure common to the metallo-β-lactamase superfamily. Tm1162 exists as a trimer in the crystal and this trimeric unit is likely to be present in solution. In the trimer, three active sites reside at the interface between subunits, suggesting that the oligomeric assembly is crucial for catalysis. A new type of structurally encoded heterodinuclear site has been identified by confirming the identity of nickel-containing heteronuclear sites in Tm1162 via X-ray absorption spectroscopy and anomalous difference Fourier maps. The second coordination sphere, including His8 and Glu73, maintains the side-chain orientations of histidines and stabilizes the metal-binding site. Nickel coordination was crucial for the oligomerization of Tm1162. The nickel-dependent and manganese-dependent β-lactamase and phosphodiesterase activities of Tm1162 have also been characterized.
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Affiliation(s)
- Hwajung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hee Jung Kim
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Atsushi Matsuura
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Bunzo Mikami
- Laboratory of Quality Design and Exploitation, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto 611-0011, Japan
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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48
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Wei J, Tong L. Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer. Nature 2015; 526:723-7. [PMID: 26458104 PMCID: PMC4838907 DOI: 10.1038/nature15375] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 08/04/2015] [Indexed: 12/13/2022]
Abstract
Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250-kilodalton (kDa), multi-domain enzymes and function as homodimers and higher oligomers. They contain a unique, 80-kDa central region that shares no homology with other proteins. Although the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known, there is currently no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500-kDa holoenzyme dimer of ScACC. The structure is remarkably different from that of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of the BC domain alone, which is a monomer. These structural changes reveal why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A and by phosphorylation of a Ser residue just before the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis.
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Affiliation(s)
- Jia Wei
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Franklin MC, Cheung J, Rudolph MJ, Burshteyn F, Cassidy M, Gary E, Hillerich B, Yao ZK, Carlier PR, Totrov M, Love JD. Structural genomics for drug design against the pathogen Coxiella burnetii. Proteins 2015; 83:2124-36. [PMID: 26033498 DOI: 10.1002/prot.24841] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 05/01/2015] [Accepted: 05/19/2015] [Indexed: 11/11/2022]
Abstract
Coxiella burnetii is a highly infectious bacterium and potential agent of bioterrorism. However, it has not been studied as extensively as other biological agents, and very few of its proteins have been structurally characterized. To address this situation, we undertook a study of critical metabolic enzymes in C. burnetii that have great potential as drug targets. We used high-throughput techniques to produce novel crystal structures of 48 of these proteins. We selected one protein, C. burnetii dihydrofolate reductase (CbDHFR), for additional work to demonstrate the value of these structures for structure-based drug design. This enzyme's structure reveals a feature in the substrate binding groove that is different between CbDHFR and human dihydrofolate reductase (hDHFR). We then identified a compound by in silico screening that exploits this binding groove difference, and demonstrated that this compound inhibits CbDHFR with at least 25-fold greater potency than hDHFR. Since this binding groove feature is shared by many other prokaryotes, the compound identified could form the basis of a novel antibacterial agent effective against a broad spectrum of pathogenic bacteria.
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Affiliation(s)
| | - Jonah Cheung
- Special Projects Division, New York Structural Biology Center, New York
| | - Michael J Rudolph
- Special Projects Division, New York Structural Biology Center, New York
| | - Fiana Burshteyn
- Special Projects Division, New York Structural Biology Center, New York
| | - Michael Cassidy
- Special Projects Division, New York Structural Biology Center, New York
| | - Ebony Gary
- Special Projects Division, New York Structural Biology Center, New York
| | - Brandan Hillerich
- Special Projects Division, New York Structural Biology Center, New York
| | - Zhong-Ke Yao
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | - Paul R Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | | | - James D Love
- Special Projects Division, New York Structural Biology Center, New York
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50
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A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins. Structure 2015; 23:2055-65. [PMID: 26439765 DOI: 10.1016/j.str.2015.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/12/2015] [Accepted: 07/22/2015] [Indexed: 01/26/2023]
Abstract
Linear repeat proteins often have high structural similarity and low (∼25%) pairwise sequence identities (PSI) among modules. We identified a unique P. anserina (Pa) sequence with tetratricopeptide repeat (TPR) homology, which contains longer (42 residue) repeats (42PRs) with an average PSI >91%. We determined the crystal structure of five tandem Pa 42PRs to 1.6 Å, and examined the stability and solution properties of constructs containing three to six Pa 42PRs. Compared with 34-residue TPRs (34PRs), Pa 42PRs have a one-turn extension of each helix, and bury more surface area. Unfolding transitions shift to higher denaturant concentration and become sharper as repeats are added. Fitted Ising models show Pa 42PRs to be more cooperative than consensus 34PRs, with increased magnitudes of intrinsic and interfacial free energies. These results demonstrate the tolerance of the TPR motif to length variation, and provide a basis to understand the effects of helix length on intrinsic/interfacial stability.
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