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Wang X, Hu S, Wang J, Zhang T, Ye K, Wen A, Zhu G, Vegas A, Zhang L, Yan W, Liu X, Liu P. Biochemical and Structural Characterization of OvoA Th2: A Mononuclear Nonheme Iron Enzyme from Hydrogenimonas thermophila for Ovothiol Biosynthesis. ACS Catal 2023; 13:15417-15426. [PMID: 38058600 PMCID: PMC10696552 DOI: 10.1021/acscatal.3c04026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Ovothiol A and ergothioneine are thiol-histidine derivatives with sulfur substitutions at the δ-carbon or ε-carbon of the l-histidine imidazole ring, respectively. Both ovothiol A and ergothioneine have protective effects on many aging-related diseases, and the sulfur substitution plays a key role in determining their chemical and biological properties, while factors governing sulfur incorporation regioselectivities in ovothiol and ergothioneine biosynthesis in the corresponding enzymes (OvoA, Egt1, or EgtB) are not yet known. In this study, we have successfully obtained the first OvoA crystal structure, which provides critical information to explain their C-S bond formation regioselectivity. Furthermore, OvoATh2 exhibits several additional activities: (1) ergothioneine sulfoxide synthase activity akin to Egt1 in ergothioneine biosynthesis; (2) cysteine dioxygenase activity using l-cysteine and l-histidine analogues as substrates; (3) cysteine dioxygenase activity upon mutation of an active site tyrosine residue (Y406). The structural insights and diverse chemistries demonstrated by OvoATh2 pave the way for future comprehensive structure-function correlation studies.
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Affiliation(s)
- Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Sha Hu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Tao Zhang
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Ke Ye
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Aiwen Wen
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Arturo Vegas
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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2
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Zhu G, Yan W, Wang X, Cheng R, Naowarojna N, Wang K, Wang J, Song H, Wang Y, Liu H, Xia X, Costello CE, Liu X, Zhang L, Liu P. Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues. JACS Au 2022; 2:1686-1698. [PMID: 35911443 PMCID: PMC9326825 DOI: 10.1021/jacsau.2c00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•CoII•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•FeII•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.
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Affiliation(s)
- Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronghai Cheng
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Kun Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Heng Song
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei Province 430072, China
| | - Yuyang Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hairong Liu
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Xuekui Xia
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Catherine E. Costello
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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3
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Stark F, Loderer C, Petchey M, Grogan G, Ansorge-Schumacher M. Advanced Insights into Catalytic and Structural Features of the Zinc-Dependent Alcohol Dehydrogenase from Thauera aromatica. Chembiochem 2022; 23:e202200149. [PMID: 35557486 PMCID: PMC9400901 DOI: 10.1002/cbic.202200149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/12/2022] [Indexed: 11/10/2022]
Abstract
The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α‐diketone 1,2‐cyclohexanedione to the corresponding α‐hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α‐substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.
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Affiliation(s)
- Frances Stark
- TU Dresden: Technische Universitat Dresden, Molecular Biotechnology, GERMANY
| | - Christoph Loderer
- TU Dresden: Technische Universitat Dresden, Molecular Biotechnology, GERMANY
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Jeong H, Lee Y, Kim J. Structural and functional characterization of TrmM in m 6 A modification of bacterial tRNA. Protein Sci 2022; 31:e4319. [PMID: 35481631 PMCID: PMC9045083 DOI: 10.1002/pro.4319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
N6 -methyladenosine (m6 A), widely distributed in both coding and noncoding RNAs, regulates the epigenetic signals and RNA metabolism in eukaryotes. Although this posttranscriptional modification is frequently observed in messenger and ribosomal RNA, it is relatively rare in transfer RNA. In Escherichia coli, TrmM encoded by yfiC is the tRNA-specific N6 methyltransferase, which modifies the A37 residue of tRNAVal (cmo5 UAC) using S-adenosyl-l-methionine as a methyl donor. However, the structure-function relationship of this enzyme is not completely understood. In this report, we determined two x-ray crystal structures of Mycoplasma capricolum TrmM with and without S-adenosyl-l-homocysteine, which is a reaction product. We also demonstrated the cellular and in vitro activities of this enzyme in the m6 A modification of tRNA and the requirement of a divalent metal ion for its function, which is unprecedented in other RNA N6 methyltransferases, including the E. coli TrmM. Our results reveal that the dimeric form of M. capricolum TrmM is important for efficient tRNA binding and catalysis, thereby offering insights into the distinct substrate specificity of the monomeric E. coli homolog.
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Affiliation(s)
- Hyeonju Jeong
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yeji Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Korea
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5
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Stachulski AV, Rossignol JF, Pate S, Taujanskas J, Robertson CM, Aerts R, Pascal E, Piacentini S, Frazia S, Santoro MG, O'Neill PM. Synthesis, antiviral activity, preliminary pharmacokinetics and structural parameters of thiazolide amine salts. Future Med Chem 2021; 13:1731-41. [PMID: 34402654 DOI: 10.4155/fmc-2021-0055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background: The thiazolides, typified by nitazoxanide, are an important class of anti-infective agents. A significant problem with nitazoxanide and its active circulating metabolite tizoxanide is their poor solubility. Results: We report the preparation and evaluation of a series of amine salts of tizoxanide and the corresponding 5-Cl thiazolide. These salts demonstrated improved aqueous solubility and absorption, as shown by physicochemical and in vivo measurements. They combine antiviral activity against influenza A virus with excellent cell safety indices. We also report the x-ray crystal structural data of the ethanolamine salt. Conclusion: The ethanol salt of thiazolide retains the activity of the parent together with an improved cell safety index, making it a good candidate for further evaluation.
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6
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Svetlov MS, Syroegin EA, Aleksandrova EV, Atkinson GC, Gregory ST, Mankin AS, Polikanov YS. Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. Nat Chem Biol 2021; 17:412-20. [PMID: 33462493 DOI: 10.1038/s41589-020-00715-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/22/2020] [Accepted: 11/18/2020] [Indexed: 01/29/2023]
Abstract
Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 Å resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally new explanation of how A2058 dimethylation confers resistance to macrolides. Moreover, high-resolution structures of two macrolide antibiotics bound to the unmodified ribosome reveal a previously unknown role of the desosamine moiety in drug binding, laying a foundation for the rational knowledge-based design of macrolides that can overcome Erm-mediated resistance.
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7
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Watanabe H, Yabe-Wada T, Onai N, Unno M. Detailed Structure of Mouse Interferon α2 and Its Interaction with Sortilin. J Biochem 2021; 170:265-273. [PMID: 33769476 DOI: 10.1093/jb/mvab038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/19/2021] [Indexed: 11/14/2022] Open
Abstract
Interferon α (IFNα) is a type I interferon, an essential cytokine employed by the immune system to fight viruses. Although a number of the structures of type I interferons have been reported, most of the known structures of IFNα are in complex with its receptors. There are only two examples of structures of free IFNα: one is a dimeric X-ray structure without side-chain information; and another is an NMR structure of human IFNα. Although we have shown that Sortilin is involved in the secretion of IFNα, the details of the molecular interaction and the secretion mechanism remain unclear. Recently, we solved the X-ray structure of mouse Sortilin, but the structure of mouse IFNα remained unknown. In the present study, we determined the crystal structure of mouse IFNα2 at 2.1 Å resolution and investigated its interaction with Sortilin. Docking simulations suggested that Arg22 of mouse IFNα2 is important for the interaction with mouse Sortilin. Mutation of Arg22 to alanine facilitated IFNα2 secretion, as determined by flow cytometry, highlighting the contribution of this residue to the interaction with Sortilin. These results suggest an important role for Arg22 in mouse IFNα for Sortilin-mediated IFNα trafficking.
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Affiliation(s)
- Honoka Watanabe
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan.,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Ibaraki 319-1106, Japan
| | - Toshiki Yabe-Wada
- Department of Immunology, Kanazawa Medical University, Kahoku Uchinada, Ishikawa 920-0293, Japan
| | - Nobuyuki Onai
- Department of Immunology, Kanazawa Medical University, Kahoku Uchinada, Ishikawa 920-0293, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan.,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Ibaraki 319-1106, Japan
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8
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Zhao Y, Feng Q, Zhou X, Zhang Y, Lukman M, Jiang J, Ruiz-Carrillo D. Mycobacterium tuberculosis puromycin hydrolase displays a prolyl oligopeptidase fold and an acyl aminopeptidase activity. Proteins 2021; 89:614-622. [PMID: 33426726 DOI: 10.1002/prot.26044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/11/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
Puromycin-hydrolizing peptidases have been described as members of the prolyl oligopeptidase peptidase family. These enzymes are present across all domains of life but still little is known of the homologs found in the pathogenic bacterium Mycobacterium tuberculosis. The crystal structure of a M. tuberculosis puromycin hydrolase peptidase has been determined at 3 Angstrom resolution, revealing a conserved prolyl oligopeptidase fold, defined by α/β-hydrolase and β-propeller domains with two distinctive loops that occlude access of large substrates to the active site. The enzyme displayed amino peptidase activity with a substrate specificity preference for hydrophobic residues in the decreasing order of phenylalanine, leucine, alanine and proline. The enzyme's active site is lined by residues Glu564 for the coordination of the substrates amino terminal moiety and His561, Val608, Tyr78, Trp306, Phe563 and Ty567 for the accommodation of hydrophobic substrates. The availability of a crystal structure for puromycin hydrolase of M. tuberculosis shall facilitate the development of inhibitors with therapeutic applications.
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Affiliation(s)
- YuanHao Zhao
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Xiao Zhou
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Yan Zhang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Maxwell Lukman
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Jie Jiang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - David Ruiz-Carrillo
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
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Maia de Oliveira T, Korboukh V, Caswell S, Winter Holt JJ, Lamb M, Hird AW, Overman R. The structure of human GCN2 reveals a parallel, back-to-back kinase dimer with a plastic DFG activation loop motif. Biochem J 2020; 477:275-84. [PMID: 31868900 DOI: 10.1042/BCJ20190196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 12/10/2019] [Accepted: 12/23/2019] [Indexed: 11/17/2022]
Abstract
When activated by amino acid starvation, the stress sensing protein kinase GCN2 phosphorylates the eukaryotic initiation factor 2 alpha, inhibiting translation to conserve energy and facilitate cell survival. Amino acid starvation, particularly of tryptophan and arginine, affects immune tolerance by suppressing differentiation and proliferation of T-cells via activation of GCN2 kinase. In addition, the GCN2 pathway mediates cancer survival directly within the context of metabolic stress. Here, we report the first crystal structures of the human GCN2 kinase domain (KD) in complex with two inhibitors of different size, shape, and chemical scaffold. Three novel activation loop conformations representative of different activation states of the kinase are described. In addition, a novel dimerization organization for GCN2 is observed. This arrangement is consistent with the hypothesis that the GCN2 KD forms an antiparallel inactive dimer until uncharged tRNA binds to it and triggers conformational changes that shift the equilibrium to the active parallel dimer.
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10
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Zhang M, Yu XW, Xu Y, Guo RT, Swapna GVT, Szyperski T, Hunt JF, Montelione GT. Structural Basis by Which the N-Terminal Polypeptide Segment of Rhizopus chinensis Lipase Regulates Its Substrate Binding Affinity. Biochemistry 2019; 58:3943-3954. [PMID: 31436959 PMCID: PMC7195698 DOI: 10.1021/acs.biochem.9b00462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of an important group of industrial enzymes, Rhizopus lipases, exhibit valuable hydrolytic features that underlie their biological functions. Particularly important is their N-terminal polypeptide segment (NTPS), which is required for secretion and proper folding but is removed in the process of enzyme maturation. A second common feature of this class of lipases is the α-helical "lid", which regulates the accessibility of the substrate to the enzyme active site. Some Rhizopus lipases also exhibit "interfacial activation" by micelle and/or aggregate surfaces. While it has long been recognized that the NTPS is critical for function, its dynamic features have frustrated efforts to characterize its structure by X-ray crystallography. Here, we combine nuclear magnetic resonance spectroscopy and X-ray crystallography to determine the structure and dynamics of Rhizopus chinensis lipase (RCL) with its 27-residue NTPS prosequence (r27RCL). Both r27RCL and the truncated mature form of RCL (mRCL) exhibit biphasic interfacial activation kinetics with p-nitrophenyl butyrate (pNPB). r27RCL exhibits a substrate binding affinity significantly lower than that of mRCL due to stabilization of the closed lid conformation by the NTPS. In contrast to previous predictions, the NTPS does not enhance lipase activity by increasing surface hydrophobicity but rather inhibits activity by forming conserved interactions with both the closed lid and the core protein structure. Single-site mutations and kinetic studies were used to confirm that the NTPS serves as internal competitive inhibitor and to develop a model of the associated process of interfacial activation. These structure-function studies provide the basis for engineering RCL lipases with enhanced catalytic activities.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People’s Republic of China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People’s Republic of China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People’s Republic of China
| | - Rey-Ting Guo
- Industrial Enzyme National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - G. V. T. Swapna
- Center for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260. USA
| | - John F. Hunt
- Department of Biological Science, Columbia University, New York, New York 10027, USA
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
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11
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Pozzi C, Ferrari S, Luciani R, Tassone G, Costi MP, Mangani S. Structural Comparison of Enterococcus faecalis and Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities. Molecules 2019; 24:E1257. [PMID: 30935102 DOI: 10.3390/molecules24071257] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 12/17/2022] Open
Abstract
Thymidylate synthase (TS) is an enzyme of paramount importance as it provides the only de novo source of deoxy-thymidine monophosphate (dTMP). dTMP, essential for DNA synthesis, is produced by the TS-catalyzed reductive methylation of 2′-deoxyuridine-5′-monophosphate (dUMP) using N5,N10-methylenetetrahydrofolate (mTHF) as a cofactor. TS is ubiquitous and a validated drug target. TS enzymes from different organisms differ in sequence and structure, but are all obligate homodimers. The structural and mechanistic differences between the human and bacterial enzymes are exploitable to obtain selective inhibitors of bacterial TSs that can enrich the currently available therapeutic tools against bacterial infections. Enterococcus faecalis is a pathogen fully dependent on TS for dTMP synthesis. In this study, we present four new crystal structures of Enterococcus faecalis and human TSs in complex with either the substrate dUMP or the inhibitor FdUMP. The results provide new clues about the half-site reactivity of Enterococcus faecalis TS and the mechanisms underlying the conformational changes occurring in the two enzymes. We also identify relevant differences in cofactor and inhibitor binding between Enterococcus faecalis and human TS that can guide the design of selective inhibitors against bacterial TSs.
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12
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Joo SH, Pemble CW, Yang EG, Raetz CRH, Chung HS. Biochemical and Structural Insights into an Fe(II)/α-Ketoglutarate/O 2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO). J Mol Biol 2018; 430:4036-4048. [PMID: 30092253 DOI: 10.1016/j.jmb.2018.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 11/18/2022]
Abstract
During lipopolysaccharide biosynthesis in several pathogens, including Burkholderia and Yersinia, 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) 3-hydroxylase, otherwise referred to as KdoO, converts Kdo to d-glycero-d-talo-oct-2-ulosonic acid (Ko) in an Fe(II)/α-ketoglutarate (α-KG)/O2-dependent manner. This conversion renders the bacterial outer membrane more stable and resistant to stresses such as an acidic environment. KdoO is a membrane-associated, deoxy-sugar hydroxylase that does not show significant sequence identity with any known enzymes, and its structural information has not been previously reported. Here, we report the biochemical and structural characterization of KdoO, Minf_1012 (KdoMI), from Methylacidiphilum infernorum V4. The de novo structure of KdoMI apoprotein indicates that KdoOMI consists of 13 α helices and 11 β strands, and has the jelly roll fold containing a metal binding motif, HXDX111H. Structures of KdoMI bound to Co(II), KdoMI bound to α-KG and Fe(III), and KdoMI bound to succinate and Fe(III), in addition to mutagenesis analysis, indicate that His146, His260, and Asp148 play critical roles in Fe(II) binding, while Arg127, Arg162, Arg174, and Trp176 stabilize α-KG. It was also observed that His225 is adjacent to the active site and plays an important role in the catalysis of KdoOMI without affecting substrate binding, possibly being involved in oxygen activation. The crystal structure of KdoOMI is the first completed structure of a deoxy-sugar hydroxylase, and the data presented here have provided mechanistic insights into deoxy-sugar hydroxylase, KdoO, and lipopolysaccharide biosynthesis.
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Affiliation(s)
- Sang Hoon Joo
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacy, Daegu Catholic University, Gyeongbuk 38430, South Korea
| | - Charles W Pemble
- Duke Macromolecular Crystallography Center, Duke University Medical Center, Durham, NC 27710, USA; Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Christian R H Raetz
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Hak Suk Chung
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea.
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Fujii T, Sato A, Okamoto Y, Yamauchi T, Kato S, Yoshida M, Oikawa T, Hata Y. The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP-10005 provides insights into the reaction mechanism of enzymes in its original family. Proteins 2016; 84:1029-42. [PMID: 27040018 DOI: 10.1002/prot.25046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 11/08/2022]
Abstract
Maleylacetate reductase plays a crucial role in catabolism of resorcinol by catalyzing the NAD(P)H-dependent reduction of maleylacetate, at a carbon-carbon double bond, to 3-oxoadipate. The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP-10005, GraC, has been elucidated by the X-ray diffraction method at 1.5 Å resolution. GraC is a homodimer, and each subunit consists of two domains: an N-terminal NADH-binding domain adopting an α/β structure and a C-terminal functional domain adopting an α-helical structure. Such structural features show similarity to those of the two existing families of enzymes in dehydroquinate synthase-like superfamily. However, GraC is distinct in dimer formation and activity expression mechanism from the families of enzymes. Two subunits in GraC have different structures from each other in the present crystal. One subunit has several ligands mimicking NADH and the substrate in the cleft and adopts a closed domain arrangement. In contrast, the other subunit does not contain any ligand causing structural changes and adopts an open domain arrangement. The structure of GraC reveals those of maleylacetate reductase both in the coenzyme, substrate-binding state and in the ligand-free state. The comparison of both subunit structures reveals a conformational change of the Tyr326 loop for interaction with His243 on ligand binding. Structures of related enzymes suggest that His243 is likely a catalytic residue of GraC. Mutational analyses of His243 and Tyr326 support the catalytic roles proposed from structural information. The crystal structure of GraC characterizes the maleylacetate reductase family as a third family in the dehydroquinate synthase-like superfamily. Proteins 2016; 84:1029-1042. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tomomi Fujii
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ai Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yuko Okamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Takae Yamauchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Shiro Kato
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Masahiro Yoshida
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Tadao Oikawa
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, 564-8680, Japan.,Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Yasuo Hata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
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14
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Obmolova G, Teplyakov A, Malia TJ, Keough E, Luo J, Sweet R, Jacobs SA, Yi F, Hippensteel R, O'Neil KT, Gilliland GL. Induced conformational change in human IL-4 upon binding of a signal-neutralizing DARPin. Proteins 2015; 83:1191-7. [PMID: 25900776 PMCID: PMC5029753 DOI: 10.1002/prot.24815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/08/2015] [Accepted: 04/11/2015] [Indexed: 11/12/2022]
Abstract
The crystal structure of DARPin 44C12V5 that neutralizes IL-4 signaling has been determined alone and bound to human IL-4. A significant conformational change occurs in the IL-4 upon DARPin binding. The DARPin binds to the face of IL-4 formed by the A and C α-helices. The structure of the DARPin remains virtually unchanged. The conformational changes in IL-4 include a reorientation of the C-helix Trp91 side chain and repositioning of CD-loop residue Leu96. Both side chains move by >9 Å, becoming buried in the central hydrophobic region of the IL-4:DARPin interface. This hydrophobic region is surrounded by a ring of hydrophilic interactions comprised of hydrogen bonds and salt bridges and represents a classical "hotspot." The structures also reveal how the DARPin neutralizes IL-4 signaling. Comparing the IL-4:DARPin complex structure with the structures of IL-4 bound to its receptors (Hage et al., Cell 1999; 97, 271-281; La Porte et al., Cell 2008, 132, 259-272), it is found that the DARPin binds to the same IL-4 face that interacts with the junction of the D1 and D2 domains of the IL-4Rα receptors. Signaling is blocked since IL-4 cannot bind to this receptor, which it must do first before initiating a productive receptor complex with either the IL-13α1 or the γc receptor.
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Affiliation(s)
- Galina Obmolova
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Alexey Teplyakov
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Thomas J. Malia
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Edward Keough
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Jinquan Luo
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Raymond Sweet
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
- Present address: Raymond Sweet's current address is 700 Oak Springs Rd.Bryn MawrPA19010
| | - Steven A. Jacobs
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Fang Yi
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Randi Hippensteel
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
- Present address: Randi Hippensteel's current address is Eurofins Lancaster Laboratories2425 New Holland PikeLancasterPA17601
| | - Karyn T. O'Neil
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
| | - Gary L. Gilliland
- Janssen Research & Development, LLC, Biotechnology Center of ExcellenceSpring HousePennsylvania19477
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15
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Almagro JC, Teplyakov A, Luo J, Sweet RW, Kodangattil S, Hernandez-Guzman F, Gilliland GL. Second antibody modeling assessment (AMA-II). Proteins 2014; 82:1553-62. [PMID: 24668560 DOI: 10.1002/prot.24567] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 01/07/2023]
Abstract
To assess the state of the art in antibody 3D modeling, 11 unpublished high-resolution x-ray Fab crystal structures from diverse species and covering a wide range of antigen-binding site conformations were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. The participants included: Accerlys Inc, Chemical Computer Group (CCG), Schrodinger, Jeff Gray's lab at John Hopkins University, Macromoltek, Astellas Pharma/Osaka University and Prediction of ImmunoGlobulin Structure (PIGS). The sequences of benchmark structures were submitted to the modelers and PIGS, and a set of models were generated for each structure. We provide here an overview of the organization, participants and main results of this second antibody modeling assessment (AMA-II). Also, we compare the results with the first antibody assessment published in this journal (Almagro et al., 2011;79:3050).
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Affiliation(s)
- Juan C Almagro
- CTI Boston, Pfizer Inc., 3 Blackfan Circle, 18 Floor, Boston, MA, 02115
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16
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Abstract
X-ray crystallography has revealed an unusual structural element in kinesin-5 motor proteins.
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Affiliation(s)
- Nikta Fakhri
- Nikta Fakhri is in the Faculty for Physics-Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
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17
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Abstract
Vault is the largest nonicosahedral cytosolic nucleoprotein particle ever described. The widespread presence and evolutionary conservation of vaults suggest important biologic roles, although their functions have not been fully elucidated. X-ray structure of vault from rat liver was determined at 3.5 Å resolution. It exhibits an ovoid shape with a size of 40 × 40 × 67 nm(3). The cage structure of vault consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The other components of vaults, telomerase-associated proteins, poly(ADP-ribose) polymerases and small RNAs, are in location in the vault particle by electron microscopy.
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Affiliation(s)
- Hideaki TANAKA
- Institute for Protein Research, Osaka University, Osaka, Japan
- PRESTO, JST, Saitama, Japan
| | - Tomitake TSUKIHARA
- Institute for Protein Research, Osaka University, Osaka, Japan
- Department of Life Science, University of Hyogo, Hyogo, Japan
- Correspondence should be addressed: T. Tsukihara, Department of Life Science, University of Hyogo, 3-2-1 Koto, Kamighori, Akoh, Hyogo 678-1297, Japan (e-mail: )
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18
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McLellan JS, Correia BE, Chen M, Yang Y, Graham BS, Schief WR, Kwong PD. Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus. J Mol Biol 2011; 409:853-66. [PMID: 21549714 PMCID: PMC3107930 DOI: 10.1016/j.jmb.2011.04.044] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/15/2011] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory tract infections in infants, but an effective vaccine has not yet been developed. An ideal vaccine would elicit protective antibodies while avoiding virus-specific T-cell responses, which have been implicated in vaccine-enhanced disease with previous RSV vaccines. We propose that heterologous proteins designed to present RSV-neutralizing antibody epitopes and to elicit cognate antibodies have the potential to fulfill these vaccine requirements, as they can be fashioned to be free of viral T-cell epitopes. Here we present the design and characterization of three epitope-scaffolds that present the epitope of motavizumab, a potent neutralizing antibody that binds to a helix-loop-helix motif in the RSV fusion glycoprotein. Two of the epitope-scaffolds could be purified, and one epitope-scaffold based on a Staphylococcus aureus protein A domain bound motavizumab with kinetic and thermodynamic properties consistent with the free epitope-scaffold being stabilized in a conformation that closely resembled the motavizumab-bound state. This epitope-scaffold was well folded as assessed by circular dichroism and isothermal titration calorimetry, and its crystal structure (determined in complex with motavizumab to 1.9 Å resolution) was similar to the computationally designed model, with all hydrogen-bond interactions critical for binding to motavizumab preserved. Immunization of mice with this epitope-scaffold failed to elicit neutralizing antibodies but did elicit sera with F binding activity. The elicitation of F binding antibodies suggests that some of the design criteria for eliciting protective antibodies without virus-specific T-cell responses are being met, but additional optimization of these novel immunogens is required.
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Affiliation(s)
- Jason S McLellan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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19
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Lim SP, Sonntag LS, Noble C, Nilar SH, Ng RH, Zou G, Monaghan P, Chung KY, Dong H, Liu B, Bodenreider C, Lee G, Ding M, Chan WL, Wang G, Jian YL, Chao AT, Lescar J, Yin Z, Vedananda TR, Keller TH, Shi PY. Small molecule inhibitors that selectively block dengue virus methyltransferase. J Biol Chem 2011; 286:6233-40. [PMID: 21147775 PMCID: PMC3057852 DOI: 10.1074/jbc.m110.179184] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 11/23/2010] [Indexed: 01/16/2023] Open
Abstract
Crystal structure analysis of Flavivirus methyltransferases uncovered a flavivirus-conserved cavity located next to the binding site for its cofactor, S-adenosyl-methionine (SAM). Chemical derivatization of S-adenosyl-homocysteine (SAH), the product inhibitor of the methylation reaction, with substituents that extend into the identified cavity, generated inhibitors that showed improved and selective activity against dengue virus methyltransferase (MTase), but not related human enzymes. Crystal structure of dengue virus MTase with a bound SAH derivative revealed that its N6-substituent bound in this cavity and induced conformation changes in residues lining the pocket. These findings demonstrate that one of the major hurdles for the development of methyltransferase-based therapeutics, namely selectivity for disease-related methyltransferases, can be overcome.
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Affiliation(s)
- Siew Pheng Lim
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | | | - Christian Noble
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Shahul H. Nilar
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Ru Hui Ng
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Gang Zou
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Paul Monaghan
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Ka Yan Chung
- the School of Biological Sciences, Nanyang Technological University, Singapore, and
| | - Hongping Dong
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Boping Liu
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | | | - Gladys Lee
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Mei Ding
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Wai Ling Chan
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Gang Wang
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Yap Li Jian
- the School of Biological Sciences, Nanyang Technological University, Singapore, and
| | | | - Julien Lescar
- the School of Biological Sciences, Nanyang Technological University, Singapore, and
| | - Zheng Yin
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - T. R. Vedananda
- the Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Thomas H. Keller
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
| | - Pei-Yong Shi
- From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore
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20
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Loll B, Rückert C, Hee CS, Saenger W, Uchanska-Ziegler B, Ziegler A. Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide. Protein Sci 2011; 20:278-90. [PMID: 21280120 PMCID: PMC3048413 DOI: 10.1002/pro.559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/10/2010] [Accepted: 11/10/2010] [Indexed: 01/07/2023]
Abstract
The human major histocompatibility complex class I antigen HLA-B*2705 binds several sequence-related peptides (pVIPR, RRKWRRWHL; pLPM2, RRRWRRLTV; pGR, RRRWHRWRL). Cross-reactivity of cytotoxic T cells (CTL) against these HLA-B*2705:peptide complexes seemed to depend on a particular peptide conformation that is facilitated by the engagement of a crucial residue within the binding groove (Asp116), associated with a noncanonical bulging-in of the middle portion of the bound peptide. We were interested whether a conformational reorientation of the ligand might contribute to the lack of cross-reactivity of these CTL with a peptide derived from voltage-dependent calcium channel α1 subunit (pCAC, SRRWRRWNR), in which the C-terminal peptide residue pArg9 could engage Asp116. Analyses of the HLA-B*2705:pCAC complex by X-ray crystallography at 1.94 Å resolution demonstrated that the peptide had indeed undergone a drastic reorientation, leading it to adopt a canonical binding mode accompanied by the loss of molecular mimicry between pCAC and sequence-related peptides such as pVIPR, pLMP2, and pGR. This was clearly a consequence of interactions of pArg9 with Asp116 and other F-pocket residues. Furthermore, we observed an unprecedented reorientation of several additional residues of the HLA-B*2705 heavy chain near the N-terminal region of the peptide, including also the presence of double conformations of two glutamate residues, Glu63 and Glu163, on opposing sides of the peptide binding groove. Together with the Arg-Ser exchange at peptide position 1, there are thus multiple structural reasons that may explain the observed failure of pVIPR-directed, HLA-B*2705-restricted CTL to cross-react with HLA-B*2705:pCAC complexes.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität BerlinTakustrasse 6, Berlin 14195, Germany,*Correspondence to: Bernhard Loll, Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, Berlin 14195, Germany. E-mail:
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Chee Seng Hee
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie, Abteilung Kristallographie, Freie Universität BerlinTakustrasse 6, Berlin 14195, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
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21
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Yamaguchi K, Okamoto N, Tokuoka K, Sugiyama S, Uchiyama N, Matsumura H, Inaka K, Urade Y, Inoue T. Structure of the inhibitor complex of old yellow enzyme from Trypanosoma cruzi. J Synchrotron Radiat 2011; 18:66-69. [PMID: 21169695 PMCID: PMC3004258 DOI: 10.1107/s0909049510033595] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Accepted: 08/20/2010] [Indexed: 05/30/2023]
Abstract
Old yellow enzyme (OYE) is an NADPH oxidoreductase which contains flavin mononucleotide as prosthetic group. The X-ray structures of OYE from Trypanosoma cruzi (TcOYE) which produces prostaglandin (PG) F(2α) from PGH(2) have been determined in the presence or absence of menadione. The binding motif of menadione, known as one of the inhibitors for TcOYE, should accelerate the structure-based development of novel anti-chagasic drugs that inhibit PGF(2α) production specifically.
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Affiliation(s)
- Keishi Yamaguchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Naoki Okamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Keiji Tokuoka
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Shigeru Sugiyama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Nahoko Uchiyama
- National Institute of Health Sciences (NIHS), Tokyo 158-8501, Japan
| | - Hiroyoshi Matsumura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Koji Inaka
- MARUWA Foods and Biosciences, Tsutsui-cho 170-1, Yamatokoriyama, Nara 639-1123, Japan
| | - Yoshihiro Urade
- Department of Molecular Behavior Biology, Osaka Bioscience Institute, Osaka 565-0874, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
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22
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Ouellet H, Kells PM, Ortiz de Montellano PR, Podust LM. Reverse type I inhibitor of Mycobacterium tuberculosis CYP125A1. Bioorg Med Chem Lett 2011; 21:332-7. [PMID: 21109436 PMCID: PMC3011832 DOI: 10.1016/j.bmcl.2010.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 11/01/2010] [Indexed: 10/18/2022]
Abstract
Cytochrome P450 CYP125A1 of Mycobacterium tuberculosis, a potential therapeutic target for tuberculosis in humans, initiates degradation of the aliphatic chain of host cholesterol and is essential for establishing M. tuberculosis infection in a mouse model of disease. We explored the interactions of CYP125A1 with a reverse type I inhibitor by X-ray structure analysis and UV-vis spectroscopy. Compound LP10 (α-[(4-methylcyclohexyl)carbonyl amino]-N-4-pyridinyl-1H-indole-3-propanamide), previously identified as a potent type II inhibitor of Trypanosomacruzi CYP51, shifts CYP125A1 to a water-coordinated low-spin state upon binding with low micromolar affinity. When LP10 is present in the active site, the crystal structure and spectral characteristics both demonstrate changes in lipophilic and electronic properties favoring coordination of the iron axial water ligand. These results provide an insight into the structural requirements for developing selective CYP125A1 inhibitors.
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Affiliation(s)
- Hugues Ouellet
- Department of Pharmaceutical Chemistry and Sandler Center for Drug Discovery, University of California, San Francisco, CA 94158, USA
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23
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Ghosh AK, Xu CX, Rao KV, Baldridge A, Agniswamy J, Wang YF, Weber IT, Aoki M, Miguel SGP, Amano M, Mitsuya H. Probing multidrug-resistance and protein-ligand interactions with oxatricyclic designed ligands in HIV-1 protease inhibitors. ChemMedChem 2010; 5:1850-4. [PMID: 20827746 PMCID: PMC3523686 DOI: 10.1002/cmdc.201000318] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Indexed: 11/12/2022]
Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
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24
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Hsieh JM, Tsirulnikov K, Sawaya MR, Magilnick N, Abuladze N, Kurtz I, Abramson J, Pushkin A. Structures of aminoacylase 3 in complex with acetylated substrates. Proc Natl Acad Sci U S A 2010; 107:17962-7. [PMID: 20921362 DOI: 10.1073/pnas.1006687107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Trichloroethylene (TCE) is one of the most widespread environmental contaminants, which is metabolized to N-acetyl-S-1,2-dichlorovinyl-L-cysteine (NA-DCVC) before being excreted in the urine. Alternatively, NA-DCVC can be deacetylated by aminoacylase 3 (AA3), an enzyme that is highly expressed in the kidney, liver, and brain. NA-DCVC deacetylation initiates the transformation into toxic products that ultimately causes acute renal failure. AA3 inhibition is therefore a target of interest to prevent TCE induced nephrotoxicity. Here we report the crystal structure of recombinant mouse AA3 (mAA3) in the presence of its acetate byproduct and two substrates: N(α)-acetyl-L-tyrosine and NA-DCVC. These structures, in conjunction with biochemical data, indicated that AA3 mediates substrate specificity through van der Waals interactions providing a dynamic interaction interface, which facilitates a diverse range of substrates.
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25
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Abstract
Aquaporins are transmembrane channels that facilitate the permeation of water and small, uncharged amphipathic molecules across cellular membranes. One distinct aquaporin subfamily contains pure water channels, whereas a second subfamily contains channels that conduct small alditols such as glycerol, in addition to water. Distinction between these substrates is central to aquaporin function, though the contributions of protein structural motifs required for selectivity are not yet fully characterized. To address this question, we sequentially engineered three signature amino acids of the glycerol-conducting subfamily into the Escherichia coli water channel aquaporin Z (AqpZ). Functional analysis of these mutant channels showed a decrease in water permeability but not the expected increase in glycerol conduction. Using X-ray crystallography, we determined the atomic resolution structures of the mutant channels. The structures revealed a channel surprisingly similar in size to the wild-type AqpZ pore. Comparison with measured rates of transport showed that, as the size of the selectivity filter region of the channel approaches that of water, channel hydrophilicity dominated water conduction energetics. In contrast, the major determinant of selectivity for larger amphipathic molecules such as glycerol was channel cross-section size. Finally, we find that, although the selectivity filter region is indeed central to substrate transport, other structural elements that do not directly interact with the substrates, such as the loop connecting helices M6 and M7, and the C loop between helices C4 and C5, play an essential role in facilitating selectivity.
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Affiliation(s)
- David F. Savage
- Graduate Group in Biophysics, and
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Joseph D. O’Connell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Larry J. W. Miercke
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Janet Finer-Moore
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Robert M. Stroud
- Graduate Group in Biophysics, and
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
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Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, Stroud RM. Function of human Rh based on structure of RhCG at 2.1 A. Proc Natl Acad Sci U S A 2010; 107:9638-43. [PMID: 20457942 PMCID: PMC2906887 DOI: 10.1073/pnas.1003587107] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In humans, NH(3) transport across cell membranes is facilitated by the Rh (rhesus) family of proteins. Human Rh C glycoprotein (RhCG) forms a trimeric complex that plays an essential role in ammonia excretion and renal pH regulation. The X-ray crystallographic structure of human RhCG, determined at 2.1 A resolution, reveals the mechanism of ammonia transport. Each monomer contains 12 transmembrane helices, one more than in the bacterial homologs. Reconstituted into proteoliposomes, RhCG conducts NH(3) to raise internal pH. Models of the erythrocyte Rh complex based on our RhCG structure suggest that the erythrocytic Rh complex is composed of stochastically assembled heterotrimers of RhAG, RhD, and RhCE.
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Affiliation(s)
- Franz Gruswitz
- Department of Biochemistry and Biophysics, S412C Genentech Hall
- Center for the Structure of Membrane Proteins, and
- Membrane Protein Expression Center, University of California, San Francisco, CA 94158
| | - Sarika Chaudhary
- Department of Biochemistry and Biophysics, S412C Genentech Hall
- Center for the Structure of Membrane Proteins, and
- Membrane Protein Expression Center, University of California, San Francisco, CA 94158
| | - Joseph D. Ho
- Department of Biochemistry and Biophysics, S412C Genentech Hall
- Center for the Structure of Membrane Proteins, and
- Membrane Protein Expression Center, University of California, San Francisco, CA 94158
| | - Avner Schlessinger
- Center for the Structure of Membrane Proteins, and
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, 503B Byers Hall, University of California, San Francisco, CA 94158; and
| | - Bobak Pezeshki
- Department of Biochemistry and Biophysics, S412C Genentech Hall
- Center for the Structure of Membrane Proteins, and
- Membrane Protein Expression Center, University of California, San Francisco, CA 94158
| | - Chi-Min Ho
- Department of Biochemistry and Biophysics, S412C Genentech Hall
- Center for the Structure of Membrane Proteins, and
- Membrane Protein Expression Center, University of California, San Francisco, CA 94158
| | - Andrej Sali
- Center for the Structure of Membrane Proteins, and
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, 503B Byers Hall, University of California, San Francisco, CA 94158; and
| | - Connie M. Westhoff
- American Red Cross, and Division of Transfusion Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19123
| | - Robert M. Stroud
- Department of Biochemistry and Biophysics, S412C Genentech Hall
- Center for the Structure of Membrane Proteins, and
- Membrane Protein Expression Center, University of California, San Francisco, CA 94158
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Elkins JM, Gileadi C, Shrestha L, Phillips C, Wang J, Muniz JRC, Doyle DA. Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms. Protein Sci 2010; 19:731-41. [PMID: 20120020 PMCID: PMC2867013 DOI: 10.1002/pro.349] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the alpha B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand.
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Affiliation(s)
| | | | | | | | | | | | - Declan A Doyle
- *Correspondence to: Declan A. Doyle, Trinity College Dublin, School of Biochemistry and Immunology, College Green, Dublin 2, Ireland. E-mail:
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Zhu N, Lightsey D, Liu J, Foroozesh M, Morgan KM, Stevens ED, Klein Stevens CL. Ethynyl and Propynylpyrene Inhibitors of Cytochrome P450. J Chem Crystallogr 2010; 40:343-352. [PMID: 20473363 PMCID: PMC2869100 DOI: 10.1007/s10870-009-9659-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The single-crystal X-ray structures and in vivo activities of three aryl acetylenic inhibitors of cytochromes P450 1A1, 1A2, 2A6, and 2B1 have been determined and are reported herein. These are 1-ethynylpyrene, 1-propy-nylpyrene, and 4-propynylpyrene. To investigate electronic influences on the mechanism of enzyme inhibition, the experimental electron density distribution of 1-ethynylpy-rene has been determined using low-temperature X-ray diffraction measurements, and the resulting net atomic charges compared with various theoretical calculations. A total of 82,390 reflections were measured with Mo Kα radiation to a (sinθ/λ)(max) = 0.985 Å(-1). Averaging symmetry equivalent reflections yielded 8,889 unique reflections. A least squares refinement procedure was used in which multipole parameters were added to describe the distortions of the atomic electron distributions from spherical symmetry. A map of the model electron density distribution of 1-ethynylpyrene was obtained. Net atomic charges calculated from refined monopole population parameters yielded charges that showed that the terminal acetylenic carbon atom (C18) is more negative than the internal carbon (C17). Net atomic charges calculated by ab initio, density functional theory, and semi-empirical methods are consistent with this trend suggesting that the terminal acetylenic carbon atom is more likely to be the site of oxidation. This is consistent with the inhibition mechanism pathway that results in the formation of a reactive ketene intermediate. This is also consistent with assay results that determined that 1-ethynylpyrene acts as a mechanism-based inhibitor of P450s 1A1 and 1A2 and as a reversible inhibitor of P450 2B1. Crystallographic data: 1-ethynylpyrene, C(18)H(10), P2(1)/c, a = 14.571(2) Å, b = 3.9094(5) Å, c = 20.242(3) Å, β = 105.042(2)°, V = 1,113.5(2) Å(3); 1-propynylpyrene, C(19)H(12), P2(1)/n, a = 8.970(2) Å, b = 10.136(1) Å, c = 14.080(3) Å, β = 99.77(2)°, V = 1,261.5(4) Å(3); 4-propynylpyrene, C(19)H(12), Pbca, a = 9.904(1) Å, b = 13.174(2) Å, c = 19.401(1) Å, V = 2,531.4(5) Å(3).
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Affiliation(s)
- Naijue Zhu
- Department of Chemistry, Xavier University of Louisiana, One Drexel Drive, New Orleans, LA 70125, USA
| | - Danielle Lightsey
- Department of Chemistry, Xavier University of Louisiana, One Drexel Drive, New Orleans, LA 70125, USA
| | - Jiawang Liu
- Department of Chemistry, Xavier University of Louisiana, One Drexel Drive, New Orleans, LA 70125, USA
| | - Maryam Foroozesh
- Department of Chemistry, Xavier University of Louisiana, One Drexel Drive, New Orleans, LA 70125, USA
| | - Kathleen M. Morgan
- Department of Chemistry, Xavier University of Louisiana, One Drexel Drive, New Orleans, LA 70125, USA
| | - Edwin D. Stevens
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
| | - Cheryl L. Klein Stevens
- Department of Chemistry, Xavier University of Louisiana, One Drexel Drive, New Orleans, LA 70125, USA
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29
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Brumshtein B, Salinas P, Peterson B, Chan V, Silman I, Sussman JL, Savickas PJ, Robinson GS, Futerman AH. Characterization of gene-activated human acid-beta-glucosidase: crystal structure, glycan composition, and internalization into macrophages. Glycobiology 2010; 20:24-32. [PMID: 19741058 PMCID: PMC2782181 DOI: 10.1093/glycob/cwp138] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Gaucher disease, the most common lysosomal storage disease, can be treated with enzyme replacement therapy (ERT), in which defective acid-beta-glucosidase (GlcCerase) is supplemented by a recombinant, active enzyme. The X-ray structures of recombinant GlcCerase produced in Chinese hamster ovary cells (imiglucerase, Cerezyme) and in transgenic carrot cells (prGCD) have been previously solved. We now describe the structure and characteristics of a novel form of GlcCerase under investigation for the treatment of Gaucher disease, Gene-Activated human GlcCerase (velaglucerase alfa). In contrast to imiglucerase and prGCD, velaglucerase alfa contains the native human enzyme sequence. All three GlcCerases consist of three domains, with the active site located in domain III. The distances between the carboxylic oxygens of the catalytic residues, E340 and E235, are consistent with distances proposed for acid-base hydrolysis. Kinetic parameters (K(m) and V(max)) of velaglucerase alfa and imiglucerase, as well as their specific activities, are similar. However, analysis of glycosylation patterns shows that velaglucerase alfa displays distinctly different structures from imiglucerase and prGCD. The predominant glycan on velaglucerase alfa is a high-mannose type, with nine mannose units, while imiglucerase contains a chitobiose tri-mannosyl core glycan with fucosylation. These differences in glycosylation affect cellular internalization; the rate of velaglucerase alfa internalization into human macrophages is at least 2-fold greater than that of imiglucerase.
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Affiliation(s)
| | - Paul Salinas
- Shire Human Genetic Therapies, Inc., Cambridge, MA, USA
| | | | - Victor Chan
- Shire Human Genetic Therapies, Inc., Cambridge, MA, USA
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | - Anthony H Futerman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel,To whom correspondence should be addressed: Tel: +972-8-9342704; Fax: +972-8-9344112; e-mail:
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30
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Johnston JB, Kells PM, Podust LM, Ortiz de Montellano PR. Biochemical and structural characterization of CYP124: a methyl-branched lipid omega-hydroxylase from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2009; 106:20687-92. [PMID: 19933331 PMCID: PMC2791619 DOI: 10.1073/pnas.0907398106] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) produces a variety of methyl-branched lipids that serve important functions, including modulating the immune response during pathogenesis and contributing to a robust cell wall that is impermeable to many chemical agents. Here, we report characterization of Mtb CYP124 (Rv2266) that includes demonstration of preferential oxidation of methyl-branched lipids. Spectrophotometric titrations and analysis of reaction products indicate that CYP124 tightly binds and hydroxylates these substrates at the chemically disfavored omega-position. We also report X-ray crystal structures of the ligand-free and phytanic acid-bound protein at a resolution of 1.5 A and 2.1 A, respectively, which provide structural insights into a cytochrome P450 with predominant omega-hydroxylase activity. The structures of ligand-free and substrate-bound CYP124 reveal several differences induced by substrate binding, including reorganization of the I helix and closure of the active site by elements of the F, G, and D helices that bind the substrate and exclude solvent from the hydrophobic active site cavity. The observed regiospecific catalytic activity suggests roles of CYP124 in the physiological oxidation of relevant Mtb methyl-branched lipids. The enzymatic specificity and structures reported here provide a scaffold for the design and testing of specific inhibitors of CYP124.
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Affiliation(s)
- Jonathan B. Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517
| | - Petrea M. Kells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517
| | - Larissa M. Podust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517
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31
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De Marco V, Gillespie PJ, Li A, Karantzelis N, Christodoulou E, Klompmaker R, van Gerwen S, Fish A, Petoukhov MV, Iliou MS, Lygerou Z, Medema RH, Blow JJ, Svergun DI, Taraviras S, Perrakis A. Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing. Proc Natl Acad Sci U S A 2009; 106:19807-12. [PMID: 19906994 PMCID: PMC2775996 DOI: 10.1073/pnas.0905281106] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Indexed: 01/12/2023] Open
Abstract
All organisms need to ensure that no DNA segments are rereplicated in a single cell cycle. Eukaryotes achieve this through a process called origin licensing, which involves tight spatiotemporal control of the assembly of prereplicative complexes (pre-RCs) onto chromatin. Cdt1 is a key component and crucial regulator of pre-RC assembly. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent DNA rereplication. Here, we address the mechanism of DNA licensing inhibition by Geminin, by combining X-ray crystallography, small-angle X-ray scattering, and functional studies in Xenopus and mammalian cells. Our findings show that the Cdt1:Geminin complex can exist in two distinct forms, a "permissive" heterotrimer and an "inhibitory" heterohexamer. Specific Cdt1 residues, buried in the heterohexamer, are important for licensing. We postulate that the transition between the heterotrimer and the heterohexamer represents a molecular switch between licensing-competent and licensing-defective states.
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Affiliation(s)
- V. De Marco
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - P. J. Gillespie
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - A. Li
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | | | - E. Christodoulou
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - R. Klompmaker
- Department of Medical Oncology and Cancer Genomics Center, Laboratory of Experimental Oncology, University Medical Center Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands; and
| | - S. van Gerwen
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - A. Fish
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - M. V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany
| | - M. S. Iliou
- Biology, Medical School, University of Patras, 26500 Rio, Patras, Greece
| | - Z. Lygerou
- Biology, Medical School, University of Patras, 26500 Rio, Patras, Greece
| | - R. H. Medema
- Department of Medical Oncology and Cancer Genomics Center, Laboratory of Experimental Oncology, University Medical Center Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands; and
| | - J. J. Blow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - D. I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | - A. Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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32
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Kolenko P, Dohnálek J, Dusková J, Skálová T, Collard R, Hasek J. New insights into intra- and intermolecular interactions of immunoglobulins: crystal structure of mouse IgG2b-Fc at 2.1-A resolution. Immunology 2009; 126:378-85. [PMID: 18783468 PMCID: PMC2669818 DOI: 10.1111/j.1365-2567.2008.02904.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 05/22/2008] [Accepted: 06/11/2008] [Indexed: 11/30/2022] Open
Abstract
The structure of the Fc fragment of monoclonal antibody IgG2b from hybridom M75 of Mus musculus has been determined by single crystal X-ray diffraction. This is the first report of the structure of the murine immunoglobulin isotype IgG2b. The structure refined at 2.1 A resolution provides more detailed structural information about native oligosaccharides than was previously available. High-quality Fourier maps provide a clear identification of alpha-l-fucose with partial occupancy in the first branch of the antennary oligosaccharides. A unique Fc:Fc interaction was observed at the C(H)2-C(H)3 interface.
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Affiliation(s)
- Petr Kolenko
- Department of Structure Analysis, Institute of Macromolecular Chemistry AS CR, Praha, Czech Republic.
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Cao J, Xu H, Zhao H, Gong W, Dunaway-Mariano D. The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis. Biochemistry 2009; 48:1293-304. [PMID: 19170545 PMCID: PMC2929599 DOI: 10.1021/bi801879z] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The focus of this paper is the hotdog-fold thioesterase THEM2 from human (hTHEM2; Swiss-Prot entry Q9NPJ3 ). In an earlier communication (Cheng, Z., Song, F., Shan, X., Wei, Z., Wang, Y., Dunaway-Mariano, D., and Gong, W. (2006) Crystal structure of human thioesterase superfamily member 2, Biochem. Biophys. Res. Commun. 349, 172-177) we reported the apo crystal structure of hTHEM2. Herein, we report the results of an extensive hTHEM2 substrate screen, the structure determination of hTHEM2 complexed with the inert substrate analogue undecan-2-one-CoA (in which OC-CH(2)-S substitutes for OC-S) and the kinetic analysis of active site mutants. The work described in this paper represents the first reported structure-function based analysis of a human hotdog-fold thioesterase. The catalytic mechanism proposed involves the Asp65/Ser83 assisted attack of a water molecule at the Gly57/Asn50 polarized thioester CO and the Asn50 assisted departure of the thiolate leaving group. Thioesterase activity was observed with acyl-CoAs but not with the human acyl-ACP or with an acyl-Cys peptide. The medium-to-long-chain fatty acyl-CoAs displayed the smallest K(m) values. The substrate specificity profile was analyzed within the context of the liganded enzyme to define the structural determinants of substrate recognition. Based on the results of this structure-function analysis we hypothesize that the physiological role of hTHEM2 involves catalysis of the hydrolysis of cytosolic medium-to-long-chain acyl-CoA thioesters.
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Affiliation(s)
- Jian Cao
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Hang Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Hong Zhao
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Weimin Gong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China,Address correspondence to: For biochemical studies: Debra Dunaway-Mariano, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, Tel: 505-277-3776, , Fax: +1 505-277-6202; For X-ray structure determination: Weimin Gong, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R., China, Tel: 8610-64888465, , Fax: +86 10 64888513
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131,Address correspondence to: For biochemical studies: Debra Dunaway-Mariano, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, Tel: 505-277-3776, , Fax: +1 505-277-6202; For X-ray structure determination: Weimin Gong, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R., China, Tel: 8610-64888465, , Fax: +86 10 64888513
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Reger AS, Wu R, Dunaway-Mariano D, Gulick AM. Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry 2008; 47:8016-25. [PMID: 18620418 PMCID: PMC2666193 DOI: 10.1021/bi800696y] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PP i, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by approximately 140 degrees to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue [Wu et al. (2008) Biochemistry 47, 8026-8039]. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.
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Affiliation(s)
- Albert S. Reger
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 144203 and Department Structural Biology, State University of New York at Buffalo, Buffalo, NY 14203, U. S. A
| | - Rui Wu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, U. S. A
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, U. S. A
| | - Andrew M. Gulick
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 144203 and Department Structural Biology, State University of New York at Buffalo, Buffalo, NY 14203, U. S. A
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35
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Ghosh AK, Xi K, Grum-Tokars V, Xu X, Ratia K, Fu W, Houser KV, Baker SC, Johnson ME, Mesecar AD. Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors. Bioorg Med Chem Lett 2007; 17:5876-80. [PMID: 17855091 PMCID: PMC2112940 DOI: 10.1016/j.bmcl.2007.08.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 10/26/2022]
Abstract
Structure-based design, synthesis, and biological evaluation of a series of peptidomimetic severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors are described. These inhibitors were designed and synthesized based upon our X-ray crystal structure of inhibitor 1 bound to SARS-CoV 3CLpro. Incorporation of Boc-Ser as the P(4)-ligand resulted in enhanced SARS-CoV 3CLpro inhibitory activity. Structural analysis of the inhibitor-bound X-ray structure revealed high binding affinity toward the enzyme.
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Affiliation(s)
- Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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36
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Bisio A, Pagano B, Romussi A, Bruno O, De Tommasi N, Romussi G, Mattia CA. Relative stereochemistry of a diterpene from Salvia cinnabarina. Molecules 2007; 12:2279-87. [PMID: 17978757 PMCID: PMC6149099 DOI: 10.3390/12102279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 10/05/2007] [Accepted: 10/05/2007] [Indexed: 11/16/2022] Open
Abstract
The relative stereochemistry of 3,4-secoisopimara-4(18),7,15-triene-3-oic acid, a diterpenoid with antispasmodic, hypotensive and antibacterial activities isolated from Salvia cinnabarina, was determined by an X-ray diffraction analysis of a single crystal of a suitable crystalline derivative.
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Affiliation(s)
- Angela Bisio
- Dipartimento di Chimica e Tecnologie Farmaceutiche e Alimentari, Università di Genova, Via Brigata Salerno, Genova, Italy
| | - Bruno Pagano
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy
| | - Alessia Romussi
- Dipartimento di Scienze Farmaceutiche, Università di Genova, Viale Benedetto XV, Genova, Italy
| | - Olga Bruno
- Dipartimento di Scienze Farmaceutiche, Università di Genova, Viale Benedetto XV, Genova, Italy
| | - Nunziatina De Tommasi
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy
| | - Giovanni Romussi
- Dipartimento di Chimica e Tecnologie Farmaceutiche e Alimentari, Università di Genova, Via Brigata Salerno, Genova, Italy
| | - Carlo Andrea Mattia
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy
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Bah A, Chen Z, Bush-Pelc LA, Mathews FS, Di Cera E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Proc Natl Acad Sci U S A 2007; 104:11603-8. [PMID: 17606903 PMCID: PMC1913866 DOI: 10.1073/pnas.0704409104] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that the cleaved form of protease-activated receptor 3 (PAR3) acts as a cofactor for thrombin cleavage and activation of PAR4 on murine platelets, but the molecular basis of this physiologically important effect remains elusive. X-ray crystal structures of murine thrombin bound to extracellular fragments of the murine receptors PAR3 ((38)SFNGGPQNTFEEFPLSDIE(56)) and PAR4 ((51)KSSDKPNPR downward arrow GYPGKFCANDSDTLELPASSQA(81), downward arrow = site of cleavage) have been solved at 2.0 and 3.5 A resolution, respectively. The cleaved form of PAR3, traced in the electron density maps from Gln-44 to Glu-56, makes extensive hydrophobic and electrostatic contacts with exosite I of thrombin through the fragment (47)FEEFPLSDIE(56). Occupancy of exosite I by PAR3 allosterically changes the conformation of the 60-loop and shifts the position of Trp-60d approximately 10 A with a resulting widening of the access to the active site. The PAR4 fragment, traced entirely in the electron density maps except for five C-terminal residues, clamps Trp-60d, Tyr-60a, and the aryl-binding site of thrombin with Pro-56 and Pro-58 at the P2 and P4 positions and engages the primary specificity pocket with Arg-59. The fragment then leaves the active site with Gly-60 and folds into a short helical turn that directs the backbone away from exosite I and over the autolysis loop. The structures demonstrate that thrombin activation of PAR4 may occur with exosite I available to bind cofactor molecules, like the cleaved form of PAR3, whose function is to promote substrate diffusion into the active site by allosterically changing the conformation of the 60-loop.
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Affiliation(s)
- Alaji Bah
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - Zhiwei Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - Leslie A. Bush-Pelc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - F. Scott Mathews
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
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Zhao D, Fei Z, Ang WH, Dyson PJ. Sulfonium-based Ionic Liquids Incorporating the Allyl Functionality. Int J Mol Sci 2007. [PMCID: PMC3685385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A series of sulfonium halides bearing allyl groups have been prepared and characterized. Anion metathesis with Li[Tf2N] and Ag[N(CN)2] resulted in sulfonium-based ionic liquids which exhibit low viscosities at room temperature. The solid state structure of one of the halide salts was determined by single crystal X-ray diffraction.
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Affiliation(s)
| | | | | | - Paul J. Dyson
- Author to whom correspondence should be addressed: , Fax: 0041-21-693-9885
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White A, Pargellis CA, Studts JM, Werneburg BG, Farmer BT. Molecular basis of MAPK-activated protein kinase 2:p38 assembly. Proc Natl Acad Sci U S A 2007; 104:6353-8. [PMID: 17395714 PMCID: PMC1851067 DOI: 10.1073/pnas.0701679104] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Indexed: 11/18/2022] Open
Abstract
p38 MAPK and MAPK-activated protein kinase 2 (MK2) are key components of signaling pathways leading to many cellular responses, notably the proinflammatory cytokine production. The physical association of p38alpha isoform and MK2 is believed to be physiologically important for this signaling. We report the 2.7-A resolution crystal structure of the unphosphorylated complex between p38alpha and MK2. These protein kinases bind "head-to-head," present their respective active sites on approximately the same side of the heterodimer, and form extensive intermolecular interactions. Among these interactions, the MK2 Ile-366-Ala-390, which includes the bipartite nuclear localization signal, binds to the p38alpha-docking region. This binding supports the involvement of noncatalytic regions to the tight binding of the MK2:p38alpha binary assembly. The MK2 residues 345-365, containing the nuclear export signal, block access to the p38alpha active site. Some regulatory phosphorylation regions of both protein kinases engage in multiple interactions with one another in this complex. This structure gives new insights into the regulation of the protein kinases p38alpha and MK2, aids in the better understanding of their known cellular and biochemical studies, and provides a basis for understanding other regulatory protein-protein interactions involving signal transduction proteins.
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Affiliation(s)
- Andre White
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA.
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40
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Conroy MJ, Durand A, Lupo D, Li XD, Bullough PA, Winkler FK, Merrick M. The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc Natl Acad Sci U S A 2007; 104:1213-8. [PMID: 17220269 PMCID: PMC1783118 DOI: 10.1073/pnas.0610348104] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Indexed: 11/18/2022] Open
Abstract
Amt proteins are ubiquitous channels for the conduction of ammonia in archaea, eubacteria, fungi, and plants. In Escherichia coli, previous studies have indicated that binding of the PII signal transduction protein GlnK to the ammonia channel AmtB regulates the channel thereby controlling ammonium influx in response to the intracellular nitrogen status. Here, we describe the crystal structure of the complex between AmtB and GlnK at a resolution of 2.5 A. This structure of PII in a complex with one of its targets reveals physiologically relevant conformations of both AmtB and GlnK. GlnK interacts with AmtB almost exclusively via a long surface loop containing Y51 (T-loop), the tip of which inserts deeply into the cytoplasmic pore exit, blocking ammonia conduction. Y51 of GlnK is also buried in the pore exit, explaining why uridylylation of this residue prevents complex formation.
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Affiliation(s)
- Matthew J. Conroy
- *Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Anne Durand
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom; and
| | - Domenico Lupo
- Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Xiao-Dan Li
- Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Per A. Bullough
- *Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Fritz K. Winkler
- Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Mike Merrick
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom; and
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41
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Hagemeier CH, Kr̈er M, Thauer RK, Warkentin E, Ermler U. Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex. Proc Natl Acad Sci U S A 2006; 103:18917-22. [PMID: 17142327 PMCID: PMC1748152 DOI: 10.1073/pnas.0603650103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Indexed: 11/18/2022] Open
Abstract
Some methanogenic and acetogenic microorganisms have the catalytic capability to cleave heterolytically the C O bond of methanol. To obtain insight into the elusive enzymatic mechanism of this challenging chemical reaction we have investigated the methanol-activating MtaBC complex from Methanosarcina barkeri composed of the zinc-containing MtaB and the 5-hydroxybenzimidazolylcobamide-carrying MtaC subunits. Here we report the 2.5-A crystal structure of this complex organized as a (MtaBC)(2) heterotetramer. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). MtaC is structurally related to the cobalamin-binding domain of methionine synthase. Its corrinoid cofactor at the top of the Rossmann domain reaches deeply into the funnel of MtaB, defining a region between zinc(II) and the corrinoid cobalt that must be the binding site for methanol. The active site geometry supports a S(N)2 reaction mechanism, in which the C O bond in methanol is activated by the strong electrophile zinc(II) and cleaved because of an attack of the supernucleophile cob(I)amide. The environment of zinc(II) is characterized by an acidic cluster that increases the charge density on the zinc(II), polarizes methanol, and disfavors deprotonation of the methanol hydroxyl group. Implications of the MtaBC structure for the second step of the reaction, in which the methyl group is transferred to coenzyme M, are discussed.
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Affiliation(s)
- Christoph H. Hagemeier
- *Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany; and
| | - Markus Kr̈er
- *Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany; and
| | - Rudolf K. Thauer
- *Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany; and
| | - Eberhard Warkentin
- Max Planck Institute for Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
| | - Ulrich Ermler
- Max Planck Institute for Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
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Coelho AC, Almeida Paz FA, Klinowski J, Pillinger M, Gonçalves IS. Microwave assisted synthesis of molybdenum and tungsten tetracarbonyl complexes with a pyrazolylpyridine ligand. Crystal structure of cis-[Mo(CO)4{ethyl[3-(2-pyridyl)-1-pyrazolyl]acetate}]. Molecules 2006; 11:940-52. [PMID: 18007398 PMCID: PMC6148560 DOI: 10.3390/11120940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 12/04/2006] [Accepted: 12/05/2006] [Indexed: 11/17/2022] Open
Abstract
We report the one-step syntheses in good yields of the complexes cis-[M(CO)4(pzpy)] {M = Mo, W; pzpy = ethyl[3-(2-pyridyl)-1-pyrazolyl]acetate} directly from the corresponding M(CO)6 starting materials by using microwave-assisted heating and reaction times of either 30 s (M = Mo) or 15 min (M = W). The structure of the molybdenum tetracarbonyl complex was determined by single crystal X-ray diffraction. The compound is monomeric and the molybdenum atom has a highly distorted octahedral geometry. The close packing of the individual cis-[Mo(CO)4(pzpy)] species is essentially driven by the need to fill the space effectively, closely mediated by weak C-H-O and pi-pi interactions.
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Affiliation(s)
- Ana C. Coelho
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Jacek Klinowski
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom; E-mail:
| | - Martyn Pillinger
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Isabel S. Gonçalves
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
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43
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Wang SX, Pandey KC, Somoza JR, Sijwali PS, Kortemme T, Brinen LS, Fletterick RJ, Rosenthal PJ, McKerrow JH. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A 2006; 103:11503-8. [PMID: 16864794 PMCID: PMC1544199 DOI: 10.1073/pnas.0600489103] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Falcipain-2 (FP2), the major cysteine protease of the human malaria parasite Plasmodium falciparum, is a hemoglobinase and promising drug target. Here we report the crystal structure of FP2 in complex with a protease inhibitor, cystatin. The FP2 structure reveals two previously undescribed cysteine protease structural motifs, designated FP2(nose) and FP2(arm), in addition to details of the active site that will help focus inhibitor design. Unlike most cysteine proteases, FP2 does not require a prodomain but only the short FP2(nose) motif to correctly fold and gain catalytic activity. Our structure and mutagenesis data suggest a molecular basis for this unique mechanism by highlighting the functional role of two Tyr within FP2(nose) and a conserved Glu outside this motif. The FP2(arm) motif is required for hemoglobinase activity. The structure reveals topographic features and a negative charge cluster surrounding FP2(arm) that suggest it may serve as an exo-site for hemoglobin binding. Motifs similar to FP2(nose) and FP2(arm) are found only in related plasmodial proteases, suggesting that they confer malaria-specific functions.
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Affiliation(s)
- Stephanie X. Wang
- *Department of Pathology and the Sandler Center, Box 2550, Byers Hall N508, and
| | - Kailash C. Pandey
- Department of Medicine, San Francisco General Hospital, Box 0811, University of California, San Francisco, CA 94143
| | - John R. Somoza
- Celera Genomics, 180 Kimball Way, South San Francisco, CA 94080
| | - Puran S. Sijwali
- Department of Medicine, San Francisco General Hospital, Box 0811, University of California, San Francisco, CA 94143
| | - Tanja Kortemme
- Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, and Departments of
| | | | - Robert J. Fletterick
- Biochemistry and Biophysics, University of California, San Francisco, CA 94143; and
| | - Philip J. Rosenthal
- Department of Medicine, San Francisco General Hospital, Box 0811, University of California, San Francisco, CA 94143
| | - James H. McKerrow
- *Department of Pathology and the Sandler Center, Box 2550, Byers Hall N508, and
- Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, and Departments of
- **To whom correspondence should be addressed. E-mail:
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44
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Natarajan K, Hicks A, Mans J, Robinson H, Guan R, Mariuzza RA, Margulies DH. Crystal structure of the murine cytomegalovirus MHC-I homolog m144. J Mol Biol 2006; 358:157-71. [PMID: 16500675 PMCID: PMC1475734 DOI: 10.1016/j.jmb.2006.01.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 12/23/2005] [Accepted: 01/05/2006] [Indexed: 10/25/2022]
Abstract
Large DNA viruses of the herpesvirus family produce proteins that mimic host MHC-I molecules as part of their immunoevasive strategy. The m144 glycoprotein, expressed by murine cytomegalovirus, is thought to be an MHC-I homolog whose expression prolongs viral survival in vivo by preventing natural killer cell activation. To explore the structural basis of this m144 function, we have determined the three-dimensional structure of an m144/beta2-microglobulin (beta2m) complex at 1.9A resolution. This structure reveals the canonical features of MHC-I molecules including readily identifiable alpha1, alpha2, and alpha3 domains. A unique disulfide bond links the alpha1 helix to the beta-sheet floor, explaining the known thermal stability of m144. Close juxtaposition of the alpha1 and alpha2 helices and the lack of critical residues that normally contribute to anchoring the peptide N and C termini eliminates peptide binding. A region of 13 amino acid residues, corresponding to the amino-terminal portion of the alpha2 helix, is missing in the electron density map, suggesting an area of structural flexibility that may be involved in ligand binding.
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Affiliation(s)
- Kannan Natarajan
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
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45
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Britton KL, Baker PJ, Fisher M, Ruzheinikov S, Gilmour DJ, Bonete MJ, Ferrer J, Pire C, Esclapez J, Rice DW. Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei. Proc Natl Acad Sci U S A 2006; 103:4846-51. [PMID: 16551747 PMCID: PMC1458758 DOI: 10.1073/pnas.0508854103] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Indexed: 11/18/2022] Open
Abstract
The structure of glucose dehydrogenase from the extreme halophile Haloferax mediterranei has been solved at 1.6-A resolution under crystallization conditions which closely mimic the "in vivo" intracellular environment. The decoration of the enzyme's surface with acidic residues is only partially neutralized by bound potassium counterions, which also appear to play a role in substrate binding. The surface shows the expected reduction in hydrophobic character, surprisingly not from changes associated with the loss of exposed hydrophobic residues but rather arising from a loss of lysines consistent with the genome wide-reduction of this residue in extreme halophiles. The structure reveals a highly ordered, multilayered solvation shell that can be seen to be organized into one dominant network covering much of the exposed surface accessible area to an extent not seen in almost any other protein structure solved. This finding is consistent with the requirement of the enzyme to form a protective shell in a dehydrating environment.
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Affiliation(s)
- K. Linda Britton
- *Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom; and
| | - Patrick J. Baker
- *Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom; and
| | - Martin Fisher
- *Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom; and
| | - Sergey Ruzheinikov
- *Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom; and
| | - D. James Gilmour
- *Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom; and
| | - María-José Bonete
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Juan Ferrer
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Julia Esclapez
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Ap. 99, E-03080 Alicante, Spain
| | - David W. Rice
- *Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom; and
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46
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Abstract
Proper assembly of large protein-RNA complexes requires sequential binding of the proteins to the RNA. The signal recognition particle (SRP) is a multiprotein-RNA complex responsible for the cotranslational targeting of proteins to biological membranes. Here we describe the crystal structure at 2.6-A resolution of the S-domain of SRP RNA from the archeon Methanococcus jannaschii. Comparison of this structure with the SRP19-bound form reveals the nature of the SRP19-induced conformational changes, which promote subsequent SRP54 attachment. These structural changes are initiated at the SRP19 binding site and transmitted through helix 6 to looped-out adenosines, which form tertiary RNA interaction with helix 8. Displacement of these adenosines enforces a conformational change of the asymmetric loop structure in helix 8. In free RNA, the three unpaired bases A195, C196, and C197 are directed toward the helical axis, whereas upon SRP19 binding the loop backbone inverts and the bases are splayed out in a conformation that resembles the SRP54-bound form. Nucleotides adjacent to the bulged nucleotides seem to be particularly important in the regulation of this loop transition. Binding of SRP19 to 7S RNA reveals an elegant mechanism of how protein-induced changes are directed through an RNA molecule and may relate to those regulating the assembly of other RNPs.
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Affiliation(s)
- Tobias Hainzl
- Umeå Centre for Molecular Pathogenesis, Umeå University, SE-901 87 Umeå, Sweden. tobias.
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47
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Nienhaus K, Nienhaus GU, Wiedenmann J, Nar H. Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP. Proc Natl Acad Sci U S A 2005; 102:9156-9. [PMID: 15964985 PMCID: PMC1166600 DOI: 10.1073/pnas.0501874102] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Indexed: 11/18/2022] Open
Abstract
Genetically encoded fusion constructs derived from fluorescent proteins (FPs) can be designed to report on a multitude of events and signals in cells, tissues, and entire organs without interfering with the complex machinery of life. EosFP is a novel FP from the scleractinian coral Lobophyllia hemprichii that switches its fluorescence emission from green (516 nm) to red (581 nm) upon irradiation with approximately 400-nm light. This property enables localized tagging of proteins and thus provides a valuable tool for tracking protein movements within live cells. Here, we present the x-ray structures of the green and red forms of WT EosFP. They reveal that formation of the red chromophore is associated with cleavage of the peptide backbone, with surprisingly little change elsewhere in the structure, and provide insights into the mechanism that generates this interesting posttranslational polypeptide modification.
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Affiliation(s)
- Karin Nienhaus
- Department of Biophysics and General Zoology, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
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48
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Su HP, Garman SC, Allison TJ, Fogg C, Moss B, Garboczi DN. The 1.51-Angstrom structure of the poxvirus L1 protein, a target of potent neutralizing antibodies. Proc Natl Acad Sci U S A 2005; 102:4240-5. [PMID: 15761054 PMCID: PMC555483 DOI: 10.1073/pnas.0501103102] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although eradicated from nature more than two decades ago, the threat of smallpox has reemerged because of concerns over its use as a biological weapon. We present the structure of the poxvirus L1 protein, a molecule that is conserved throughout the poxvirus family and is nearly identical in vaccinia virus and in variola virus, which causes smallpox. L1 is a myristoylated envelope protein that is a potent target for neutralizing antibodies and an important component of current experimental vaccines. The L1 structure reveals a hydrophobic cavity located adjacent to its N terminus. The cavity would be capable of shielding the myristate moiety, which is essential for virion assembly. The structure of L1 is a step in the elucidation of molecular mechanisms common to all poxviruses that may stimulate the design of safer vaccines and new antipoxvirus drugs.
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Affiliation(s)
- Hua-Poo Su
- Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA
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49
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Page R, Peti W, Wilson IA, Stevens RC, Wüthrich K. NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc Natl Acad Sci U S A 2005; 102:1901-5. [PMID: 15677718 PMCID: PMC548552 DOI: 10.1073/pnas.0408490102] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the Joint Center for Structural Genomics, one-dimensional (1D) 1H NMR spectroscopy is routinely used to characterize the folded state of protein targets and, thus, serves to guide subsequent crystallization efforts and to identify proteins for NMR structure determination. Here, we describe 1D 1H NMR screening of a group of 79 mouse homologue proteins, which correlates the NMR data with the outcome of subsequent crystallization experiments and crystallographic structure determination. Based on the 1D 1H NMR spectra, the proteins are classified into four groups, "A" to "D." A-type proteins are candidates for structure determination by NMR or crystallography; "B"-type are earmarked for crystallography; "C" indicates folded globular proteins with broadened line shapes; and "D" are nonglobular, "unfolded" polypeptides. The results obtained from coarse- and fine-screen crystallization trials imply that only A- and B-type proteins should be used for extensive crystallization trials in the future, with C and D proteins subjected only to coarse-screen crystallization trials. Of the presently studied 79 soluble protein targets, 63% yielded A- or B-quality 1D 1H NMR spectra. Although similar yields of crystallization hits were obtained for all four groups, A to D, crystals from A- and B-type proteins diffracted on average to significantly higher resolution than crystals produced from C- or D-type proteins. Furthermore, the output of refined crystal structures from this test set of proteins was 4-fold higher for A- and B-type than for C- and D-type proteins.
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Affiliation(s)
- Rebecca Page
- Department of Molecular Biology and Joint Center for Structural Genomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Calderone V, Dolderer B, Hartmann HJ, Echner H, Luchinat C, Del Bianco C, Mangani S, Weser U. The crystal structure of yeast copper thionein: the solution of a long-lasting enigma. Proc Natl Acad Sci U S A 2005; 102:51-6. [PMID: 15613489 PMCID: PMC544076 DOI: 10.1073/pnas.0408254101] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Indexed: 11/18/2022] Open
Abstract
We report here the crystal structure of yeast copper thionein (Cu-MT), determined at 1.44-A resolution. The Cu-MT structure shows the largest known oligonuclear Cu(I) thiolate cluster in biology, consisting of six trigonally and two digonally coordinated Cu(I) ions. This is at variance with the results from previous spectroscopic determinations, which were performed on MT samples containing seven rather than eight metal ions. The protein backbone has a random coil structure with the loops enfolding the copper cluster, which is located in a cleft where it is bound to 10 cysteine residues. The protein structure is somewhat different from that of Ag(7)-MT and similar, but not identical, to that of Cu(7)-MT. Besides the different structure of the metal cluster, the main differences lie in the cysteine topology and in the conformation of some portions of the backbone. The present structure suggests that Cu-MT, in addition to its role as a safe depository for copper ions in the cell, may play an active role in the delivery of copper to metal-free chaperones.
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Affiliation(s)
- Vito Calderone
- Department of Chemistry, University of Siena, Via Aldo Moro, 53100 Siena, Italy
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