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Choi Y, Koh J, Cha SS, Roe JH. Activation of zinc uptake regulator by zinc binding to three regulatory sites. Nucleic Acids Res 2024; 52:4185-4197. [PMID: 38349033 PMCID: PMC11077047 DOI: 10.1093/nar/gkae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 05/09/2024] Open
Abstract
Zur is a Fur-family metalloregulator that is widely used to control zinc homeostasis in bacteria. In Streptomyces coelicolor, Zur (ScZur) acts as both a repressor for zinc uptake (znuA) gene and an activator for zinc exporter (zitB) gene. Previous structural studies revealed three zinc ions specifically bound per ScZur monomer; a structural one to allow dimeric architecture and two regulatory ones for DNA-binding activity. In this study, we present evidence that Zur contains a fourth specific zinc-binding site with a key histidine residue (H36), widely conserved among actinobacteria, for regulatory function. Biochemical, genetic, and calorimetric data revealed that H36 is critical for hexameric binding of Zur to the zitB zurbox and further binding to its upstream region required for full activation. A comprehensive thermodynamic model demonstrated that the DNA-binding affinity of Zur to both znuA and zitB zurboxes is remarkably enhanced upon saturation of all three regulatory zinc sites. The model also predicts that the strong coupling between zinc binding and DNA binding equilibria of Zur drives a biphasic activation of the zitB gene in response to a wide concentration change of zinc. Similar mechanisms may be pertinent to other metalloproteins, expanding their response spectrum through binding multiple regulatory metals.
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Affiliation(s)
- Yunchan Choi
- Laboratory of Molecular Microbiology, School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Junseock Koh
- Laboratory of Biophysical Chemistry, School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun-Shin Cha
- Protein Research Laboratory, Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jung-Hye Roe
- Laboratory of Molecular Microbiology, School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
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2
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Baksheeva VE, Tiulina VV, Iomdina EN, Petrov SY, Filippova OM, Kushnarevich NY, Suleiman EA, Eyraud R, Devred F, Serebryakova MV, Shebardina NG, Chistyakov DV, Senin II, Mitkevich VA, Tsvetkov PO, Zernii EY. Tear nanoDSF Denaturation Profile Is Predictive of Glaucoma. Int J Mol Sci 2023; 24:ijms24087132. [PMID: 37108298 PMCID: PMC10139145 DOI: 10.3390/ijms24087132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/07/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is a frequent blindness-causing neurodegenerative disorder characterized by optic nerve and retinal ganglion cell damage most commonly due to a chronic increase in intraocular pressure. The preservation of visual function in patients critically depends on the timeliness of detection and treatment of the disease, which is challenging due to its asymptomatic course at early stages and lack of objective diagnostic approaches. Recent studies revealed that the pathophysiology of glaucoma includes complex metabolomic and proteomic alterations in the eye liquids, including tear fluid (TF). Although TF can be collected by a non-invasive procedure and may serve as a source of the appropriate biomarkers, its multi-omics analysis is technically sophisticated and unsuitable for clinical practice. In this study, we tested a novel concept of glaucoma diagnostics based on the rapid high-performance analysis of the TF proteome by differential scanning fluorimetry (nanoDSF). An examination of the thermal denaturation of TF proteins in a cohort of 311 ophthalmic patients revealed typical profiles, with two peaks exhibiting characteristic shifts in POAG. Clustering of the profiles according to peaks maxima allowed us to identify glaucoma in 70% of cases, while the employment of artificial intelligence (machine learning) algorithms reduced the amount of false-positive diagnoses to 13.5%. The POAG-associated alterations in the core TF proteins included an increase in the concentration of serum albumin, accompanied by a decrease in lysozyme C, lipocalin-1, and lactotransferrin contents. Unexpectedly, these changes were not the only factor affecting the observed denaturation profile shifts, which considerably depended on the presence of low-molecular-weight ligands of tear proteins, such as fatty acids and iron. Overall, we recognized the TF denaturation profile as a novel biomarker of glaucoma, which integrates proteomic, lipidomic, and metallomic alterations in tears, and monitoring of which could be adapted for rapid non-invasive screening of the disease in a clinical setting.
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Affiliation(s)
- Viktoriia E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
- Institut Neurophysiopathol, INP, Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ, CNRS, 13005 Marseille, France
| | - Veronika V Tiulina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Elena N Iomdina
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Sergey Yu Petrov
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Olga M Filippova
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Nina Yu Kushnarevich
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Elena A Suleiman
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Rémi Eyraud
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023 Saint-Etienne, France
| | - François Devred
- Institut Neurophysiopathol, INP, Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ, CNRS, 13005 Marseille, France
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Natalia G Shebardina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Dmitry V Chistyakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Ivan I Senin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Philipp O Tsvetkov
- Institut Neurophysiopathol, INP, Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ, CNRS, 13005 Marseille, France
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
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3
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Cornish KAS, Lange J, Aevarsson A, Pohl E. CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins. J Biol Chem 2022; 298:101919. [PMID: 35405098 PMCID: PMC9108980 DOI: 10.1016/j.jbc.2022.101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
The Candidate Phyla Radiation is a recently uncovered and vast expansion of the bacterial domain of life, made up of largely uncharacterized phyla that lack isolated representatives. This unexplored territory of genetic diversity presents an abundance of novel proteins with potential applications in the life-science sectors. Here, we present the structural and functional elucidation of CPR-C4, a hypothetical protein from the genome of a thermophilic Candidate Phyla Radiation organism, identified through metagenomic sequencing. Our analyses revealed that CPR-C4 is a member of a family of highly conserved proteins within the Candidate Phyla Radiation. The function of CPR-C4 as a cysteine protease was predicted through remote structural similarity to the Homo sapiens vasohibins and subsequently confirmed experimentally with fluorescence-based activity assays. Furthermore, detailed structural and sequence alignment analysis enabled identification of a noncanonical cysteine-histidine-leucine(carbonyl) catalytic triad. The unexpected structural and functional similarities between CPR-C4 and the human vasohibins suggest an evolutionary relationship undetectable at the sequence level alone.
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Affiliation(s)
- Katy A S Cornish
- Department of Chemistry, Durham University, Lower Mountjoy, Durham, County Durham, United Kingdom
| | | | | | - Ehmke Pohl
- Department of Chemistry, Durham University, Lower Mountjoy, Durham, County Durham, United Kingdom; Department of Biosciences, Durham University, Upper Mountjoy, Durham, County Durham, United Kingdom.
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4
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Chaussavoine I, Isabet T, Lener R, Montaville P, Vasireddi R, Chavas LMG. Implementation of wedged-serial protein crystallography at PROXIMA-1. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:439-446. [PMID: 35254307 PMCID: PMC8900848 DOI: 10.1107/s1600577521013242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
An approach for serial crystallography experiments based on wedged-data collection is described. This is an alternative method for recording in situ X-ray diffraction data on crystalline samples efficiently loaded in an X-ray compatible microfluidic chip. Proper handling of the microfluidic chip places crystalline samples at geometrically known positions with respect to the focused X-ray interaction area for serial data collection of small wedges. The integration of this strategy takes advantage of the greatly modular sample environment available on the endstation, which allows access to both in situ and more classical cryo-crystallography with minimum time loss. The method represents another optional data collection approach that adds up to the already large set of methods made available to users. Coupled with the advances in processing serial crystallography data, the wedged-data collection strategy proves highly efficient in minimizing the amount of required sample crystals for recording a complete dataset. From the advances in microfluidic technology presented here, high-throughput room-temperature crystallography experiments may become routine and should be easily extended to industrial use.
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Affiliation(s)
| | | | - Robin Lener
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
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5
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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6
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis. Angew Chem Int Ed Engl 2021; 60:19766-19773. [DOI: 10.1002/anie.202103872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/04/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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7
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Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants. Sci Rep 2021; 11:9647. [PMID: 33958623 PMCID: PMC8102479 DOI: 10.1038/s41598-021-88920-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 11/09/2022] Open
Abstract
The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme–HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively. The calculated sequence similarity networks between HISN2 analogs from prokaryotes and eukaryotes suggest that the plant enzymes are closest relatives of those in the class of Deltaproteobacteria. In this work, we obtained crystal structures of HISN2 enzyme from Medicago truncatula (MtHISN2) and described its architecture and interactions with AMP. The AMP molecule bound to the PRA-PH domain shows positioning of the N1-phosphoribosyl relevant to catalysis. AMP bound to the PRA-CH domain mimics a part of the substrate, giving insights into the reaction mechanism. The latter interaction also arises as a possible second-tier regulatory mechanism of the HBP flux, as indicated by inhibition assays and isothermal titration calorimetry.
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8
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Trastoy B, Naegeli A, Anso I, Sjögren J, Guerin ME. Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun 2020; 11:4844. [PMID: 32973204 PMCID: PMC7518263 DOI: 10.1038/s41467-020-18696-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.
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Affiliation(s)
- Beatriz Trastoy
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | | | - Itxaso Anso
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | | | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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9
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Zhang J, Zhao L, Seo HS, Jung JH, Choi JI, Kim MK, Lim S. Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1. Biochem Biophys Res Commun 2019; 513:354-359. [PMID: 30961930 DOI: 10.1016/j.bbrc.2019.03.209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 12/11/2022]
Abstract
Deinococcus radiodurans is an extremophilic bacterium well-known for its extraordinary resistance to ionizing radiation and other DNA damage- and oxidative stress-generating agents. In addition to its efficient DNA damage repair and oxidative stress resistance mechanisms, protein family expansions and stress-induced genes/proteins are also regarded as important components that add to the robustness of this bacterium. D. radiodurans encodes specific expansions of 13 DinB/YfiT homologs, which is a relatively large number when compared to those found in Gram-positive bacteria. In this study, we investigated the expression profiles of 13 dinB genes after γ-irradiation, mitomycin C and H2O2 treatment. dr0053 had the highest expression levels after DNA-damage inducing γ-irradiation and MMC treatment, increasing ∼200-fold and ∼16-fold, respectively. We also determined the crystal structure of DR0053 at 2.07 Å resolution. DR0053 adopted a typical four-helix bundle structure that is characteristic of DinB/YfiT proteins. A putative metal binding site was occupied by zinc even though the highly conserved His triad of DinB/YfiT proteins was replaced by Glu-Asn-His.
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Affiliation(s)
- Jing Zhang
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Lei Zhao
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ho Seong Seo
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Min-Kyu Kim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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10
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Hou C, Tsodikov OV. Utilizing guanine-coordinated Zn 2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:32-40. [PMID: 30644843 DOI: 10.1107/s205979831801553x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/02/2018] [Indexed: 11/10/2022]
Abstract
The experimental phase determination of crystal structures of nucleic acids and nucleic acid-ligand complexes would benefit from a facile method. Even for double-stranded DNA, software-generated models are generally insufficiently accurate to serve as molecular replacement search models, necessitating experimental phasing. Here, it is demonstrated that Zn2+ ions coordinated to the N7 atom of guanine bases generate sufficient anomalous signal for single-wavelength anomalous diffraction (SAD) phasing of DNA crystal structures. Using zinc SAD, three crystal structures of double-stranded DNA oligomers, 5'-AGGGATCCCT-3', 5'-GGGATCCC-3' and 5'-GAGGCCTC-3', were determined. By determining the crystal structure of one of these oligomers, GAGGCCTC, in the presence of Mg2+ instead of Zn2+, it was demonstrated that Zn2+ is not structurally perturbing. These structures allowed the analysis of structural changes in the DNA on the binding of analogues of the natural product mithramycin to two of these oligomers, AGGGATCCCT and GAGGCCTC. Zinc SAD may become a routine approach for determining the crystal structures of nucleic acids and their complexes with small molecules.
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Affiliation(s)
- Caixia Hou
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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11
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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12
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Jo I, Kim D, Bang YJ, Ahn J, Choi SH, Ha NC. The hydrogen peroxide hypersensitivity of OxyR2 in Vibrio vulnificus depends on conformational constraints. J Biol Chem 2017; 292:7223-7232. [PMID: 28264933 DOI: 10.1074/jbc.m116.743765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 02/18/2017] [Indexed: 12/11/2022] Open
Abstract
Most Gram-negative bacteria respond to excessive levels of H2O2 using the peroxide-sensing transcriptional regulator OxyR, which can induce the expression of antioxidant genes to restore normality. Vibrio vulnificus has two distinct OxyRs (OxyR1 and OxyR2), which are sensitive to different levels of H2O2 and induce expression of two different peroxidases, Prx1 and Prx2. Although OxyR1 has both high sequence similarity and H2O2 sensitivity comparable with that of other OxyR proteins, OxyR2 exhibits limited sequence similarity and is more sensitive to H2O2 To investigate the basis for this difference, we determined crystal structures and carried out biochemical analyses of OxyR2. The determined structure of OxyR2 revealed a flipped conformation of the peptide bond before Glu-204, a position occupied by glycine in other OxyR proteins. Activity assays showed that the sensitivity to H2O2 was reduced to the level of other OxyR proteins by the E204G mutation. We solved the structure of the OxyR2-E204G mutant with the same packing environment. The structure of the mutant revealed a dual conformation of the peptide bond before Gly-204, indicating the structural flexibility of the region. This structural duality extended to the backbone atoms of Gly-204 and the imidazole ring of His-205, which interact with H2O2 and invariant water molecules near the peroxidatic cysteine, respectively. Structural comparison suggests that Glu-204 in OxyR2 provides rigidity to the region that is important in H2O2 sensing, compared with the E204G structure or other OxyR proteins. Our findings provide a structural basis for the higher sensitivity of OxyR2 to H2O2 and also suggest a molecular mechanism for bacterial regulation of expression of antioxidant genes at divergent concentrations of cellular H2O2.
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Affiliation(s)
- Inseong Jo
- From the Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agriculture and Life Sciences, and
| | - Dukyun Kim
- From the Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agriculture and Life Sciences, and.,the National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Ye-Ji Bang
- From the Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agriculture and Life Sciences, and.,the National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Jinsook Ahn
- From the Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agriculture and Life Sciences, and
| | - Sang Ho Choi
- From the Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agriculture and Life Sciences, and .,the National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Nam-Chul Ha
- From the Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agriculture and Life Sciences, and
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13
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Sohn YS, Lee SG, Lee KH, Ku B, Shin HC, Cha SS, Kim YG, Lee HS, Kang SG, Oh BH. Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase. PLoS One 2016; 11:e0167549. [PMID: 27907125 PMCID: PMC5132392 DOI: 10.1371/journal.pone.0167549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/16/2016] [Indexed: 11/19/2022] Open
Abstract
A hypothetical protein TON_0340 of a Thermococcus species is a protein conserved in a variety of organisms including human. Herein, we present four different crystal structures of TON_0340, leading to the identification of an active-site cavity harboring a metal-binding site composed of six invariant aspartate and glutamate residues that coordinate one to three metal ions. Biochemical and mutational analyses involving many phosphorous compounds show that TON_0340 is a Mn2+-dependent phosphatase. Mg2+ binds to TON_0340 less tightly and activates the phosphatase activity less efficiently than Mn2+. Whereas Ca2+ and Zn2+ are able to bind to the protein, they are unable to activate its enzymatic activity. Since the active-site cavity is small and largely composed of nearly invariant stretches of 11 or 13 amino acids, the physiological substrates of TON_0340 and its homologues are likely to be a small and the same molecule. The Mn2+-bound TON_0340 structure provides a canonical model for the ubiquitously present TON_0340 homologues and lays a strong foundation for the elucidation of their substrate and biological function.
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Affiliation(s)
- Young-Sik Sohn
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Seong-Gyu Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Kwang-Hoon Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Sung-Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
- * E-mail:
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14
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Xing L, Lin K, Zhou X, Liu S, Luo Y. Multistate Mechanism of Lysozyme Denaturation through Synchronous Analysis of Raman Spectra. J Phys Chem B 2016; 120:10660-10667. [DOI: 10.1021/acs.jpcb.6b07900] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Ke Lin
- School
of Physics and Optoelectronic Engineering, Xidian University, Xi’an, Shanxi 710071, China
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15
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Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction. J Bacteriol 2016; 198:1218-29. [PMID: 26833410 DOI: 10.1128/jb.00872-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bacteriophytochrome photoreceptors (BphPs) and their cognate response regulators make up two-component signal transduction systems which direct bacteria to mount phenotypic responses to changes in environmental light quality. Most of these systems utilize single-domain response regulators to transduce signals through unknown pathways and mechanisms. Here we describe the photocycle and autophosphorylation kinetics of RtBphP1, a red light-regulated histidine kinase from the desert bacterium Ramlibacter tataouinensis RtBphP1 undergoes red to far-red photoconversion with rapid thermal reversion to the dark state. RtBphP1 is autophosphorylated in the dark; this activity is inhibited under red light. The RtBphP1 cognate response regulator, the R. tataouinensis bacteriophytochrome response regulator (RtBRR), and a homolog, AtBRR from Agrobacterium tumefaciens, crystallize unexpectedly as arm-in-arm dimers, reliant on a conserved hydrophobic motif, hFWAhL (where h is a hydrophobic M, V, L, or I residue). RtBRR and AtBRR dimerize distinctly from four structurally characterized phytochrome response regulators found in photosynthetic organisms and from all other receiver domain homodimers in the Protein Data Bank. A unique cacodylate-zinc-histidine tag metal organic framework yielded single-wavelength anomalous diffraction phases and may be of general interest. Examination of the effect of the BRR stoichiometry on signal transduction showed that phosphorylated RtBRR is accumulated more efficiently than the engineered monomeric RtBRR (RtBRRmon) in phosphotransfer reactions. Thus, we conclude that arm-in-arm dimers are a relevant signaling intermediate in this class of two-component regulatory systems. IMPORTANCE BphP histidine kinases and their cognate response regulators comprise widespread red light-sensing two-component systems. Much work on BphPs has focused on structural understanding of light sensing and on enhancing the natural infrared fluorescence of these proteins, rather than on signal transduction or the resultant phenotypes. To begin to address this knowledge gap, we solved the crystal structures of two single-domain response regulators encoded by a region immediately downstream of that encoding BphPs. We observed a previously unknown arm-in-arm dimer linkage. Monomerization via deletion of the C-terminal dimerization motif had an inhibitory effect on net response regulator phosphorylation, underlining the importance of these unusual dimers for signal transduction.
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16
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Kim JS, Song S, Lee M, Lee S, Lee K, Ha NC. Crystal Structure of a Soluble Fragment of the Membrane Fusion Protein HlyD in a Type I Secretion System of Gram-Negative Bacteria. Structure 2016; 24:477-85. [DOI: 10.1016/j.str.2015.12.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 10/22/2022]
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17
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Bokhove M, Sadat Al Hosseini H, Saito T, Dioguardi E, Gegenschatz-Schmid K, Nishimura K, Raj I, de Sanctis D, Han L, Jovine L. Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins. J Struct Biol 2016; 194:1-7. [PMID: 26850170 PMCID: PMC4771870 DOI: 10.1016/j.jsb.2016.01.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/28/2016] [Accepted: 01/31/2016] [Indexed: 01/19/2023]
Abstract
We present a strategy to obtain milligrams of highly post-translationally modified eukaryotic proteins, transiently expressed in mammalian cells as rigid or cleavable fusions with a mammalianized version of bacterial maltose-binding protein (mMBP). This variant was engineered to combine mutations that enhance MBP solubility and affinity purification, as well as provide crystal-packing interactions for increased crystallizability. Using this cell type-independent approach, we could increase the expression of secreted and intracellular human proteins up to 200-fold. By molecular replacement with MBP, we readily determined five novel high-resolution structures of rigid fusions of targets that otherwise defied crystallization.
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Affiliation(s)
- Marcel Bokhove
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Hamed Sadat Al Hosseini
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Takako Saito
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Elisa Dioguardi
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Katharina Gegenschatz-Schmid
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Kaoru Nishimura
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Isha Raj
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | | | - Ling Han
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Luca Jovine
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden.
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18
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Kim JS, Yoon BY, Ahn J, Cha J, Ha NC. Crystal structure of β-N-acetylglucosaminidase CbsA from Thermotoga neapolitana. Biochem Biophys Res Commun 2015; 464:869-74. [DOI: 10.1016/j.bbrc.2015.07.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
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19
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Kim HS, Kim J, Im HN, An DR, Lee M, Hesek D, Mobashery S, Kim JY, Cho K, Yoon HJ, Han BW, Lee BI, Suh SW. Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2800-12. [PMID: 25372672 PMCID: PMC4220969 DOI: 10.1107/s1399004714018732] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/18/2014] [Indexed: 01/01/2023]
Abstract
Helicobacter pylori infection causes a variety of gastrointestinal diseases, including peptic ulcers and gastric cancer. Its colonization of the gastric mucosa of the human stomach is a prerequisite for survival in the stomach. Colonization depends on its motility, which is facilitated by the helical shape of the bacterium. In H. pylori, cross-linking relaxation or trimming of peptidoglycan muropeptides affects the helical cell shape. Csd4 has been identified as one of the cell shape-determining peptidoglycan hydrolases in H. pylori. It is a Zn(2+)-dependent D,L-carboxypeptidase that cleaves the bond between the γ-D-Glu and the mDAP of the non-cross-linked muramyltripeptide (muramyl-L-Ala-γ-D-Glu-mDAP) of the peptidoglycan to produce the muramyldipeptide (muramyl-L-Ala-γ-D-Glu) and mDAP. Here, the crystal structure of H. pylori Csd4 (HP1075 in strain 26695) is reported in three different states: the ligand-unbound form, the substrate-bound form and the product-bound form. H. pylori Csd4 consists of three domains: an N-terminal D,L-carboxypeptidase domain with a typical carboxypeptidase fold, a central β-barrel domain with a novel fold and a C-terminal immunoglobulin-like domain. The D,L-carboxypeptidase domain recognizes the substrate by interacting primarily with the terminal mDAP moiety of the muramyltripeptide. It undergoes a significant structural change upon binding either mDAP or the mDAP-containing muramyltripeptide. It it also shown that Csd5, another cell-shape determinant in H. pylori, is capable of interacting not only with H. pylori Csd4 but also with the dipeptide product of the reaction catalyzed by Csd4.
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Affiliation(s)
- Hyoun Sook Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jieun Kim
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Na Im
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Doo Ri An
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Kun Cho
- Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Il Lee
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Gyeonggi 410-769, Republic of Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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20
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Heine A, Herrmann G, Selmer T, Terwesten F, Buckel W, Reuter K. High resolution crystal structure of Clostridium propionicum β-alanyl-CoA:ammonia lyase, a new member of the "hot dog fold" protein superfamily. Proteins 2014; 82:2041-53. [PMID: 24623648 DOI: 10.1002/prot.24557] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/21/2014] [Accepted: 03/06/2014] [Indexed: 11/11/2022]
Abstract
Clostridium propionicum is the only organism known to ferment β-alanine, a constituent of coenzyme A (CoA) and the phosphopantetheinyl prosthetic group of holo-acyl carrier protein. The first step in the fermentation is a CoA-transfer to β-alanine. Subsequently, the resulting β-alanyl-CoA is deaminated by the enzyme β-alanyl-CoA:ammonia lyase (Acl) to reversibly form ammonia and acrylyl-CoA. We have determined the crystal structure of Acl in its apo-form at a resolution of 0.97 Å as well as in complex with CoA at a resolution of 1.59 Å. The structures reveal that the enyzme belongs to a superfamily of proteins exhibiting a so called "hot dog fold" which is characterized by a five-stranded antiparallel β-sheet with a long α-helix packed against it. The functional unit of all "hot dog fold" proteins is a homodimer containing two equivalent substrate binding sites which are established by the dimer interface. In the case of Acl, three functional dimers combine to a homohexamer strongly resembling the homohexamer formed by YciA-like acyl-CoA thioesterases. Here, we propose an enzymatic mechanism based on the crystal structure of the Acl·CoA complex and molecular docking.
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Affiliation(s)
- Andreas Heine
- Institut für Pharmazeutische Chemie, Fachbereich Pharmazie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032, Marburg, Germany
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21
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Experimental phasing using zinc and sulfur anomalous signals measured at the zinc absorption peak. J Microbiol 2013; 51:639-43. [PMID: 24173644 DOI: 10.1007/s12275-013-3412-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/27/2013] [Indexed: 10/26/2022]
Abstract
Iron is an essential transition metal required for bacterial growth and survival. Excess free iron can lead to the generation of reactive oxygen species that can cause severe damage to cellular functions. Cells have developed iron-sensing regulators to maintain iron homeostasis at the transcription level. The ferric uptake regulator (Fur) is an iron-responsive regulator that controls the expression of genes involved in iron homeostasis, bacterial virulence, stress resistance, and redox metabolism. Here, we report the expression, purification, crystallization, and phasing of the apo-form of Bacillus subtilis Fur (BsFur) in the absence of regulatory metal ions. Crystals were obtained by microbatch crystallization method at 295 K and diffraction data at a resolution of 2.6 Å was collected at the zinc peak wavelength (λ=1.2823 Å). Experimental phasing identified the positions of one zinc atom and four sulfur atoms of cysteine residues coordinating the zinc atom, indicating that the data contained a meaningful anomalous scattering originating from the ordered zinc-coordinating sulfur atoms, in spite of the small anomalous signals of sulfur atoms at the examined wavelength.
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22
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Otten H, Michalak M, Mikkelsen JD, Larsen S. The binding of zinc ions to Emericella nidulans endo-β-1,4-galactanase is essential for crystal formation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:850-4. [PMID: 23908026 PMCID: PMC3729157 DOI: 10.1107/s1744309113019714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/16/2013] [Indexed: 11/10/2022]
Abstract
A novel Emericella nidulans endo-β-1,4-galactanase (EnGAL) demonstrates a strong capacity to generate high levels of very potent prebiotic oligosaccharides from potato pulp, a by-product of the agricultural potato-starch industry. EnGAL belongs to glycoside hydrolase family 53 and shows high (72.5%) sequence identity to an endo-β-1,4-galactanase from Aspergillus aculeatus. Diffraction data extending to 2.0 Å resolution were collected from a crystal of EnGAL grown from conditions containing 0.2 M zinc acetate. The crystal structure showed a high similarity between EnGAL and other endo-β-1,4-galactanases belonging to GH53. It also revealed 15 zinc ions bound to the protein, one of which is located in the active site, where it is coordinated by residues Glu136 and Glu246 which comprise the catalytic machinery. The majority of the zinc ions are located on the surface of the enzyme, in some cases with side chains from two different molecules as ligands, thus explaining why the presence of zinc ions was essential for crystallization.
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Affiliation(s)
- Harm Otten
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Malwina Michalak
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltoft Plads, Building 229, DK-2800 Kongens Lyngby, Denmark
| | - Jørn Dalgaard Mikkelsen
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltoft Plads, Building 229, DK-2800 Kongens Lyngby, Denmark
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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23
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Kim MK, Lee S, An YJ, Jeong CS, Ji CJ, Lee JW, Cha SS. In-house zinc SAD phasing at Cu Kα edge. Mol Cells 2013; 36:74-81. [PMID: 23686432 PMCID: PMC3887929 DOI: 10.1007/s10059-013-0074-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022] Open
Abstract
De novo zinc single-wavelength anomalous dispersion (Zn-SAD) phasing has been demonstrated with the 1.9 Å resolution data of glucose isomerase and 2.6 Å resolution data of Staphylococcus aureus Fur (SaFur) collected using in-house Cu Kα X-ray source. The successful in-house Zn-SAD phasing of glucose isomerase, based on the anomalous signals of both zinc ions introduced to crystals by soaking and native sulfur atoms, drove us to determine the structure of SaFur, a zinc-containing transcription factor, by Zn-SAD phasing using in-house X-ray source. The abundance of zinc-containing proteins in nature, the easy zinc derivatization of the protein surface, no need of synchrotron access, and the successful experimental phasing with the modest 2.6 Å resolution SAD data indicate that inhouse Zn-SAD phasing can be widely applicable to structure determination.
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Affiliation(s)
- Min-Kyu Kim
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Sangmin Lee
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
- Ocean Science and Technology School, Pusan 606-791,
Korea
| | - Young Jun An
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Chang-Sook Jeong
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Chang-Jun Ji
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul 133-791,
Korea
| | - Jin-Won Lee
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul 133-791,
Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
- Ocean Science and Technology School, Pusan 606-791,
Korea
- Department of Marine Biotechnology, University of Science and Technology, Daejeon 305-333
Korea
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