1
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Jiao M, He W, Ouyang Z, Yu Q, Zhang J, Qin Q, Wang R, Guo X, Liu R, He X, Hwang PM, Zheng F, Wen Y. Molybdate uptake interplay with ROS tolerance modulates bacterial pathogenesis. SCIENCE ADVANCES 2025; 11:eadq9686. [PMID: 39813328 PMCID: PMC11734730 DOI: 10.1126/sciadv.adq9686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 12/13/2024] [Indexed: 01/18/2025]
Abstract
The rare metal element molybdenum functions as a cofactor in molybdoenzymes that are essential to life in almost all living things. Molybdate can be captured by the periplasmic substrate-binding protein ModA of ModABC transport system in bacteria. We demonstrate that ModA plays crucial roles in growth, multiple metabolic pathways, and ROS tolerance in Acinetobacter baumannii. Crystal structures of molybdate-coordinated A. baumannii ModA show a noncanonical disulfide bond with a conformational change between reduced and oxidized states. Disulfide bond formation reduced binding affinity to molybdate by two orders of magnitude and contributes to its substrate preference. ModA-mediated molybdate binding was important for A. baumannii infection in a murine pneumonia model. Together, our study sheds light on the structural and functional diversity of molybdate uptake and highlights a potential target for antibacterial development.
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Affiliation(s)
- Min Jiao
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Wenbo He
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Zhenlin Ouyang
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Qinyue Yu
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Jiaxin Zhang
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
| | - Qian Qin
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Ruochen Wang
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Xiaolong Guo
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Ruihan Liu
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
| | - Xiaoyu He
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peter M. Hwang
- Departments of Medicine and Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Fang Zheng
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
| | - Yurong Wen
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710061, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
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2
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Jung H, Jiang V, Su Z, Inaba Y, Khoury FF, Banta S. Overexpression of a Designed Mutant Oxyanion Binding Protein ModA/WtpA in Acidithiobacillus ferrooxidans for the Low pH Recovery of Molybdenum and Rhenium. JACS AU 2024; 4:2957-2965. [PMID: 39211588 PMCID: PMC11350598 DOI: 10.1021/jacsau.4c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 09/04/2024]
Abstract
Molybdenum and rhenium are critically important metals for a number of emerging technologies. We identified and characterized a molybdenum/tungsten transport protein (ModA/WtpA) of Acidithiobacillus ferrooxidans and demonstrated the binding of tungstate, molybdate, and chromate. We used computational design to expand the binding capabilities of the protein to include perrhenate. A disulfide bond was engineered into the binding pocket of ModA/WtpA to introduce a more favorable geometric coordination and surface charge distribution for oxyanion binding. The mutant protein experimentally demonstrated a 2-fold higher binding affinity for molybdate and 6-fold higher affinity for perrhenate. The overexpression of the wild-type and mutant ModA/WtpA proteins in A. ferrooxidans cells enhanced the innate tungstate, molybdate, and chromate binding capacities of the cells to up to 2-fold higher. In addition, the engineered cells expressing the mutant protein exhibited enhanced perrhenate binding, showing 5-fold and 2-fold higher binding capacities compared to the wild-type and ModA/WtpA-overexpressing cells, respectively. Furthermore, the engineered cell lines enhanced biocorrosion of stainless steel as well as the recovered valuable metals from an acidic wastewater generated from molybdenite processing. The improved binding efficiency for the oxyanion metals, along with the high selectivity over nontargeted metals under mixed metal environments, highlights the potential value of the engineered strains for practical microbial metal reclamation under low pH conditions.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New
York, New York 10027, United States
| | - Virginia Jiang
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New
York, New York 10027, United States
| | - Zihang Su
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New
York, New York 10027, United States
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New
York, New York 10027, United States
| | - Farid F. Khoury
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New
York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New
York, New York 10027, United States
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3
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Maiuolo L, Tallarida MA, Meduri A, Fiorani G, Jiritano A, De Nino A, Algieri V, Costanzo P. 1,2,3-Triazole Hybrids Containing Isatins and Phenolic Moieties: Regioselective Synthesis and Molecular Docking Studies. Molecules 2024; 29:1556. [PMID: 38611835 PMCID: PMC11013233 DOI: 10.3390/molecules29071556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
The synthesis of hybrid molecules is one of the current strategies of drug discovery for the development of new lead compounds. The 1,2,3-triazole moiety represents an important building block in Medicinal Chemistry, extensively present in recent years. In this paper, we presented the design and the synthesis of new 1,2,3-triazole hybrids, containing both an isatine and a phenolic core. Firstly, the non-commercial azide and the alkyne synthons were prepared by different isatines and phenolic acids, respectively. Then, the highly regioselective synthesis of 1,4-disubstituted triazoles was obtained in excellent yields by a click chemistry approach, catalyzed by Cu(I). Finally, a molecular docking study was performed on the hybrid library, finding four different therapeutic targets. Among them, the most promising results were obtained on 5-lipoxygenase, an enzyme involved in the inflammatory processes.
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Affiliation(s)
- Loredana Maiuolo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy; (L.M.); (A.J.); (A.D.N.)
| | | | - Angelo Meduri
- RINA Consulting—Centro Sviluppo Materiali SpA, Zona Industriale San Pietro Lametino, Comparto 1, 88046 Lamezia Terme, CZ, Italy;
| | - Giulia Fiorani
- Department Molecular Sciences and Nanosystems, University Ca’ Foscari Venezia, 30172 Mestre, VE, Italy;
| | - Antonio Jiritano
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy; (L.M.); (A.J.); (A.D.N.)
| | - Antonio De Nino
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy; (L.M.); (A.J.); (A.D.N.)
| | - Vincenzo Algieri
- IRCCS NEUROMED—Istituto Neurologico Mediterraneo, Via Atinense 18, 86077 Pozzilli, IS, Italy
| | - Paola Costanzo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy; (L.M.); (A.J.); (A.D.N.)
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4
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Maunders EA, Ngu DHY, Ganio K, Hossain SI, Lim BYJ, Leeming MG, Luo Z, Tan A, Deplazes E, Kobe B, McDevitt CA. The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis. Front Microbiol 2022; 13:903146. [PMID: 35685933 PMCID: PMC9171197 DOI: 10.3389/fmicb.2022.903146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bryan Y. J. Lim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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5
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Bioinformatics analysis and biochemical characterisation of ABC transporter-associated periplasmic substrate-binding proteins ModA and MetQ from Helicobacter pylori strain SS1. Biophys Chem 2021; 272:106577. [PMID: 33756269 DOI: 10.1016/j.bpc.2021.106577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 12/29/2022]
Abstract
The human gastric pathogen Helicobacter pylori relies on the uptake of host-provided nutrients for its proliferation and pathogenicity. ABC transporters that mediate import of small molecules into the cytoplasm of H. pylori employ their cognate periplasmic substrate-binding proteins (SBPs) for ligand capture in the periplasm. The genome of the mouse-adapted strain SS1 of H. pylori encodes eight ABC transporter-associated SBPs, but little is known about their specificity or structure. In this study, we demonstrated that the SBP annotated as ModA binds molybdate (MoO42-, KD = 3.8 nM) and tungstate (WO42-, KD = 7.8 nM). In addition, we showed that MetQ binds D-methionine (KD = 9.5 μM), but not L-methionine, which suggests the existence of as yet unknown pathway for L-methionine uptake. Homology modelling has led to identification of the ligand-binding residues.
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6
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Zhong Q, Kobe B, Kappler U. Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria. Front Microbiol 2020; 11:615860. [PMID: 33362753 PMCID: PMC7759655 DOI: 10.3389/fmicb.2020.615860] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.
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Affiliation(s)
- Qifeng Zhong
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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7
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Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Front Microbiol 2020; 11:587127. [PMID: 33193240 PMCID: PMC7604516 DOI: 10.3389/fmicb.2020.587127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
A nitrate- and metal-contaminated site at the Oak Ridge Reservation (ORR) was previously shown to contain the metal molybdenum (Mo) at picomolar concentrations. This potentially limits microbial nitrate reduction, as Mo is required by the enzyme nitrate reductase, which catalyzes the first step of nitrate removal. Enrichment for anaerobic nitrate-reducing microbes from contaminated sediment at the ORR yielded Bacillus strain EB106-08-02-XG196. This bacterium grows in the presence of multiple metals (Cd, Ni, Cu, Co, Mn, and U) but also exhibits better growth compared to control strains, including Pseudomonas fluorescens N2E2 isolated from a pristine ORR environment under low molybdate concentrations (<1 nM). Molybdate is taken up by the molybdate binding protein, ModA, of the molybdate ATP-binding cassette transporter. ModA of XG196 is phylogenetically distinct from those of other characterized ModA proteins. The genes encoding ModA from XG196, P. fluorescens N2E2 and Escherichia coli K12 were expressed in E. coli and the recombinant proteins were purified. Isothermal titration calorimetry analysis showed that XG196 ModA has a higher affinity for molybdate than other ModA proteins with a molybdate binding constant (KD) of 2.2 nM, about one order of magnitude lower than those of P. fluorescens N2E2 (27.0 nM) and E. coli K12 (25.0 nM). XG196 ModA also showed a fivefold higher affinity for molybdate than for tungstate (11 nM), whereas the ModA proteins from P. fluorescens N2E2 [KD (Mo) 27.0 nM, KD (W) 26.7 nM] and E. coli K12[(KD (Mo) 25.0 nM, KD (W) 23.8 nM] had similar affinities for the two oxyanions. We propose that high molybdate affinity coupled with resistance to multiple metals gives strain XG196 a competitive advantage in Mo-limited environments contaminated with high concentrations of metals and nitrate, as found at ORR.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Torben Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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8
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Dos Santos RN, Bottino GF, Gozzo FC, Morcos F, Martínez L. Structural complementarity of distance constraints obtained from chemical cross-linking and amino acid coevolution. Proteins 2019; 88:625-632. [PMID: 31693206 DOI: 10.1002/prot.25843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/07/2019] [Accepted: 11/03/2019] [Indexed: 12/11/2022]
Abstract
The analysis of amino acid coevolution has emerged as a practical method for protein structural modeling by providing structural contact information from alignments of amino acid sequences. In parallel, chemical cross-linking/mass spectrometry (XLMS) has gained attention as a universally applicable method for obtaining low-resolution distance constraints to model the quaternary arrangements of proteins, and more recently even protein tertiary structures. Here, we show that the structural information obtained by XLMS and coevolutionary analysis are effectively complementary: the distance constraints obtained by each method are almost exclusively associated with non-coincident pairs of residues, and modeling results obtained by the combination of both sets are improved relative to considering the same total number of constraints of a single type. The structural rationale behind the complementarity of the distance constraints is discussed and illustrated for a representative set of proteins with different sizes and folds.
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Affiliation(s)
- Ricardo N Dos Santos
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,Center for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Guilherme F Bottino
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,Center for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fábio C Gozzo
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas.,Department of Bioengineering, University of Texas at Dallas, Richardson, Texas
| | - Leandro Martínez
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,Center for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo, Brazil
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9
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Mandal SK, Adhikari R, Sharma A, Chandravanshi M, Gogoi P, Kanaujia SP. Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8. Metallomics 2019; 11:597-612. [DOI: 10.1039/c8mt00374b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquisition of different metal ions by metal uptake ABC transporters of Thermus thermophilus HB8 for accomplishing its various cellular functions.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Rahi Adhikari
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Anjaney Sharma
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Monika Chandravanshi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
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10
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Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry 2018; 57:5864-5876. [PMID: 30204415 PMCID: PMC6189639 DOI: 10.1021/acs.biochem.8b00783] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-, and tetrasaccharides. Two of these proteins (tmMBP1 and tmMBP2) share significant sequence identity, approximately 90%, while the third (tmMBP3) shares less than 40% identity. MBP from Escherichia coli (ecMBP) shares 35% sequence identity with the tmMBPs. This subset of MBP isoforms offers an interesting opportunity to investigate the mechanisms underlying the evolution of substrate specificity and affinity profiles in a genome where redundant MBP genes are present. In this study, the X-ray crystal structures of tmMBP1, tmMBP2, and tmMBP3 are reported in the absence and presence of oligosaccharides. tmMBP1 and tmMBP2 have binding pockets that are larger than that of tmMBP3, enabling them to bind to larger substrates, while tmMBP1 and tmMBP2 also undergo substrate-induced hinge bending motions (∼52°) that are larger than that of tmMBP3 (∼35°). Small-angle X-ray scattering was used to compare protein behavior in solution, and computer simulations provided insights into dynamics of these proteins. Comparing quantitative protein-substrate interactions and dynamical properties of tmMBPs with those of the promiscuous ecMBP and disaccharide selective Thermococcus litoralis MBP provides insights into the features that enable selective binding. Collectively, the results provide insights into how the structure and dynamics of tmMBP homologues enable them to differentiate between a myriad of chemical entities while maintaining their common fold.
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Affiliation(s)
- Shantanu Shukla
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
| | - Caeley Gullett
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dean A. A. Myles
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Deparment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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11
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Radka CD, DeLucas LJ, Wilson LS, Lawrenz MB, Perry RD, Aller SG. Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites. Acta Crystallogr D Struct Biol 2017; 73:557-572. [PMID: 28695856 PMCID: PMC5505154 DOI: 10.1107/s2059798317006349] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/26/2017] [Indexed: 01/05/2023] Open
Abstract
Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.
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Affiliation(s)
- Christopher D. Radka
- Graduate Biomedical Sciences Microbiology Theme, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lawrence J. DeLucas
- Office of the Provost, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Landon S. Wilson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matthew B. Lawrenz
- Department of Microbiology and Immunology and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Robert D. Perry
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Dekker L, Arsène-Ploetze F, Santini JM. Comparative proteomics of Acidithiobacillus ferrooxidans grown in the presence and absence of uranium. Res Microbiol 2016; 167:234-9. [DOI: 10.1016/j.resmic.2016.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/07/2015] [Indexed: 10/22/2022]
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13
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Bairagya HR, Bansal M. New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study. Proteins 2016; 84:360-73. [PMID: 26756917 DOI: 10.1002/prot.24983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/06/2015] [Accepted: 12/19/2015] [Indexed: 11/11/2022]
Abstract
Human Guanine Monophosphate Synthetase (hGMPS) converts XMP to GMP, and acts as a bifunctional enzyme with N-terminal "glutaminase" (GAT) and C-terminal "synthetase" domain. The enzyme is identified as a potential target for anti-cancer and immunosuppressive therapies. GAT domain of enzyme plays central role in metabolism, and contains conserved catalytic residues Cys104, His190, and Glu192. MD simulation studies on GAT domain suggest that position of oxyanion in unliganded conformation is occupied by one conserved water molecule (W1), which also stabilizes that pocket. This position is occupied by a negatively charged atom of the substrate or ligand in ligand bound crystal structures. In fact, MD simulation study of Ser75 to Val indicates that W1 conserved water molecule is stabilized by Ser75, while Thr152, and His190 also act as anchor residues to maintain appropriate architecture of oxyanion pocket through water mediated H-bond interactions. Possibly, four conserved water molecules stabilize oxyanion hole in unliganded state, but they vacate these positions when the enzyme (hGMPS)-substrate complex is formed. Thus this study not only reveals functionally important role of conserved water molecules in GAT domain, but also highlights essential role of other non-catalytic residues such as Ser75 and Thr152 in this enzymatic domain. The results from this computational study could be of interest to experimental community and provide a testable hypothesis for experimental validation. Conserved sites of water molecules near and at oxyanion hole highlight structural importance of water molecules and suggest a rethink of the conventional definition of chemical geometry of inhibitor binding site.
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Affiliation(s)
- Hridoy R Bairagya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Tejada-Jiménez M, Schwarz G. Molybdenum and Tungsten. BINDING, TRANSPORT AND STORAGE OF METAL IONS IN BIOLOGICAL CELLS 2014. [DOI: 10.1039/9781849739979-00223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molybdenum (Mo) is an essential micronutrient for the majority of organisms ranging from bacteria to animals. To fulfil its biological role, it is incorporated into a pterin-based Mo-cofactor (Moco) and can be found in the active centre of more than 50 enzymes that are involved in key reactions of carbon, nitrogen and sulfur metabolism. Five of the Mo-enzymes are present in eukaryotes: nitrate reductase (NR), sulfite oxidase (SO), aldehyde oxidase (AO), xanthine oxidase (XO) and the amidoxime-reducing component (mARC). Cells acquire Mo in form of the oxyanion molybdate using specific molybdate transporters. In bacteria, molybdate transport is an extensively studied process and is mediated mainly by the ATP-binding cassette system ModABC. In contrast, in eukaryotes, molybdate transport is poorly understood since specific molybdate transporters remained unknown until recently. Two rather distantly related families of proteins, MOT1 and MOT2, are involved in eukaryotic molybdate transport. They each feature high-affinity molybdate transporters that regulate the intracellular concentration of Mo and thus control activity of Mo-enzymes. The present chapter presents an overview of the biological functions of Mo with special focus on recent data related to its uptake, binding and storage.
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Affiliation(s)
- Manuel Tejada-Jiménez
- Institute of Biochemistry, Department of Chemistry, University of Cologne Zuelpicher Str. 47 Cologne 50674 Germany
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne Zuelpicher Str. 47 Cologne 50674 Germany
- Center for Molecular Medicine Cologne, University of Cologne Robert-Koch Str. 21 Cologne 50931 Germany
- Cluster of Excellence in Ageing Research, CECAD Research Center Joseph-Stelzmann-Str. 26 Cologne 50931 Germany
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16
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TupA: a tungstate binding protein in the periplasm of Desulfovibrio alaskensis G20. Int J Mol Sci 2014; 15:11783-98. [PMID: 24992597 PMCID: PMC4139814 DOI: 10.3390/ijms150711783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/29/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022] Open
Abstract
The TupABC system is involved in the cellular uptake of tungsten and belongs to the ABC (ATP binding cassette)-type transporter systems. The TupA component is a periplasmic protein that binds tungstate anions, which are then transported through the membrane by the TupB component using ATP hydrolysis as the energy source (the reaction catalyzed by the ModC component). We report the heterologous expression, purification, determination of affinity binding constants and crystallization of the Desulfovibrio alaskensis G20 TupA. The tupA gene (locus tag Dde_0234) was cloned in the pET46 Enterokinase/Ligation-Independent Cloning (LIC) expression vector, and the construct was used to transform BL21 (DE3) cells. TupA expression and purification were optimized to a final yield of 10 mg of soluble pure protein per liter of culture medium. Native polyacrylamide gel electrophoresis was carried out showing that TupA binds both tungstate and molybdate ions and has no significant interaction with sulfate, phosphate or perchlorate. Quantitative analysis of metal binding by isothermal titration calorimetry was in agreement with these results, but in addition, shows that TupA has higher affinity to tungstate than molybdate. The protein crystallizes in the presence of 30% (w/v) polyethylene glycol 3350 using the hanging-drop vapor diffusion method. The crystals diffract X-rays beyond 1.4 Å resolution and belong to the P21 space group, with cell parameters a = 52.25 Å, b = 42.50 Å, c = 54.71 Å, β = 95.43°. A molecular replacement solution was found, and the structure is currently under refinement.
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Rice AJ, Harrison A, Alvarez FJD, Davidson AL, Pinkett HW. Small substrate transport and mechanism of a molybdate ATP binding cassette transporter in a lipid environment. J Biol Chem 2014; 289:15005-13. [PMID: 24722984 PMCID: PMC4031551 DOI: 10.1074/jbc.m114.563783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Embedded in the plasma membrane of all bacteria, ATP binding cassette (ABC) importers facilitate the uptake of several vital nutrients and cofactors. The ABC transporter, MolBC-A, imports molybdate by passing substrate from the binding protein MolA to a membrane-spanning translocation pathway of MolB. To understand the mechanism of transport in the biological membrane as a whole, the effects of the lipid bilayer on transport needed to be addressed. Continuous wave-electron paramagnetic resonance and in vivo molybdate uptake studies were used to test the impact of the lipid environment on the mechanism and function of MolBC-A. Working with the bacterium Haemophilus influenzae, we found that MolBC-A functions as a low affinity molybdate transporter in its native environment. In periods of high extracellular molybdate concentration, H. influenzae makes use of parallel molybdate transport systems (MolBC-A and ModBC-A) to take up a greater amount of molybdate than a strain with ModBC-A alone. In addition, the movement of the translocation pathway in response to nucleotide binding and hydrolysis in a lipid environment is conserved when compared with in-detergent analysis. However, electron paramagnetic resonance spectroscopy indicates that a lipid environment restricts the flexibility of the MolBC translocation pathway. By combining continuous wave-electron paramagnetic resonance spectroscopy and substrate uptake studies, we reveal details of molybdate transport and the logistics of uptake systems that employ multiple transporters for the same substrate, offering insight into the mechanisms of nutrient uptake in bacteria.
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Affiliation(s)
- Austin J Rice
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Alistair Harrison
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus Ohio 43205, and
| | | | - Amy L Davidson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Heather W Pinkett
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208,
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18
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A specific interdomain interaction preserves the structural and binding properties of the ModA protein from the phytopathogen Xanthomonas citri domain interaction and transport in ModA. Arch Biochem Biophys 2013; 539:20-30. [PMID: 24035743 DOI: 10.1016/j.abb.2013.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 10/26/2022]
Abstract
The periplasmic-binding proteins in ATP-binding cassette systems (ABC Transporters) are responsible for the capture and delivery of ligands to their specific transporters, triggering a series of ATP-driven conformational changes that leads to the transport of the ligand. Structurally consisting of two lobes, the proteins change conformation after interaction with the ligand. The structure of the molybdate-binding protein (ModA) from Xanthomonas citri, bound to molybdate, was previously solved by our group and an interdomain interaction, mediated by a salt bridge between K127 and D59, apparently supports the binding properties and keeps the domains closed. To determinate the importance of this interaction, we built two ModA mutants, K127S and D59A, and analysed their functional and structural properties. Based on a set of spectroscopic experiments, crystallisation trials, structure determination and molecular dynamics (MD) simulations, we showed that the salt bridge is essential to maintain the structure and binding properties. Additionally, the MD simulations revealed that this mutant adopted a more compact structure that packed down the ligand-binding pocket. From the closed bound to open structure, the positioning of the helices forming the dipole and the salt bridge are essential to induce an intermediate state.
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19
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Pratte BS, Sheridan R, James JA, Thiel T. Regulation of V-nitrogenase genes inAnabaena variabilisby RNA processing and by dual repressors. Mol Microbiol 2013; 88:413-24. [DOI: 10.1111/mmi.12197] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Brenda S. Pratte
- University of Missouri - St. Louis; Dept. of Biology; Research 223; St. Louis; MO; 63121; USA
| | - Ryan Sheridan
- University of Missouri - St. Louis; Dept. of Biology; Research 223; St. Louis; MO; 63121; USA
| | - Jessie A. James
- University of Missouri - St. Louis; Dept. of Biology; Research 223; St. Louis; MO; 63121; USA
| | - Teresa Thiel
- University of Missouri - St. Louis; Dept. of Biology; Research 223; St. Louis; MO; 63121; USA
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20
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Tirado-Lee L, Lee A, Rees DC, Pinkett HW. Classification of a Haemophilus influenzae ABC transporter HI1470/71 through its cognate molybdate periplasmic binding protein, MolA. Structure 2011; 19:1701-10. [PMID: 22078568 PMCID: PMC3258573 DOI: 10.1016/j.str.2011.10.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/11/2011] [Accepted: 10/09/2011] [Indexed: 01/07/2023]
Abstract
molA (HI1472) from H. influenzae encodes a periplasmic binding protein (PBP) that delivers substrate to the ABC transporter MolB(2)C(2) (formerly HI1470/71). The structures of MolA with molybdate and tungstate in the binding pocket were solved to 1.6 and 1.7 Å resolution, respectively. The MolA-binding protein binds molybdate and tungstate, but not other oxyanions such as sulfate and phosphate, making it the first class III molybdate-binding protein structurally solved. The ∼100 μM binding affinity for tungstate and molybdate is significantly lower than observed for the class II ModA molybdate-binding proteins that have nanomolar to low micromolar affinity for molybdate. The presence of two molybdate loci in H. influenzae suggests multiple transport systems for one substrate, with molABC constituting a low-affinity molybdate locus.
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Affiliation(s)
- Leidamarie Tirado-Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Allen Lee
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Heather W. Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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22
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A molecular basis for tungstate selectivity in prokaryotic ABC transport systems. J Bacteriol 2011; 193:4999-5001. [PMID: 21784948 DOI: 10.1128/jb.05056-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The essential trace compounds tungstate and molybdate are taken up by cells via ABC transporters. Despite their similar ionic radii and chemical properties, the WtpA protein selectively binds tungstate in the presence of molybdate. Using site-directed mutagenesis of conserved binding pocket residues, we established a molecular basis for tungstate selectivity.
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23
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24
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Aguilar-Barajas E, Díaz-Pérez C, Ramírez-Díaz MI, Riveros-Rosas H, Cervantes C. Bacterial transport of sulfate, molybdate, and related oxyanions. Biometals 2011; 24:687-707. [PMID: 21301930 DOI: 10.1007/s10534-011-9421-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 01/26/2011] [Indexed: 12/29/2022]
Affiliation(s)
- Esther Aguilar-Barajas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Edificio B-3, Ciudad Universitaria, 58030 Morelia, Michoacan, Mexico
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25
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Chan S, Giuroiu I, Chernishof I, Sawaya MR, Chiang J, Gunsalus RP, Arbing MA, Perry LJ. Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:242-50. [PMID: 20208152 PMCID: PMC2833028 DOI: 10.1107/s1744309109055158] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/22/2009] [Indexed: 11/10/2022]
Abstract
The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 A resolution and in the molybdate-bound conformation at 2.25 and 2.45 A resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed alpha/beta domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the 'Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins.
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Affiliation(s)
- Sum Chan
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Iulia Giuroiu
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Irina Chernishof
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Janet Chiang
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Robert P. Gunsalus
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
- The Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Mark A. Arbing
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - L. Jeanne Perry
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
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26
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Smart JP, Cliff MJ, Kelly DJ. A role for tungsten in the biology of Campylobacter jejuni: tungstate stimulates formate dehydrogenase activity and is transported via an ultra-high affinity ABC system distinct from the molybdate transporter. Mol Microbiol 2009; 74:742-57. [PMID: 19818021 DOI: 10.1111/j.1365-2958.2009.06902.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The food-borne pathogen Campylobacter jejuni possesses no known tungstoenzymes, yet encodes two ABC transporters (Cj0300-0303 and Cj1538-1540) homologous to bacterial molybdate (ModABC) uptake systems and the tungstate transporter (TupABC) of Eubacterium acidaminophilum respectively. The actual substrates and physiological role of these transporters were investigated. Tryptophan fluorescence spectroscopy and isothermal titration calorimetry of the purified periplasmic binding proteins of each system revealed that while Cj0303 is unable to discriminate between molybdate and tungstate (K(D) values for both ligands of 4-8 nM), Cj1540 binds tungstate with a K(D) of 1.0 +/- 0.2 pM; 50 000-fold more tightly than molybdate. Induction-coupled plasma mass spectroscopy of single and double mutants showed that this large difference in affinity is reflected in a lower cellular tungsten content in a cj1540 (tupA) mutant compared with a cj0303c (modA) mutant. Surprisingly, formate dehydrogenase (FDH) activity was decreased approximately 50% in the tupA strain, and supplementation of the growth medium with tungstate significantly increased FDH activity in the wild type, while inhibiting known molybdoenzymes. Our data suggest that C. jejuni possesses a specific, ultra-high affinity tungstate transporter that supplies tungsten for incorporation into FDH. Furthermore, possession of two MoeA paralogues may explain the formation of both molybdopterin and tungstopterin in this bacterium.
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Affiliation(s)
- Jonathan P Smart
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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27
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Duhme‐Klair A. From Siderophores and Self‐Assembly to Luminescent Sensors: The Binding of Molybdenum by Catecholamides. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900416] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Hollenstein K, Comellas-Bigler M, Bevers LE, Feiters MC, Meyer-Klaucke W, Hagedoorn PL, Locher KP. Distorted octahedral coordination of tungstate in a subfamily of specific binding proteins. J Biol Inorg Chem 2009; 14:663-72. [PMID: 19234723 DOI: 10.1007/s00775-009-0479-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 02/04/2009] [Indexed: 11/30/2022]
Abstract
Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). These substrates are captured by an external, high-affinity binding protein, and delivered to ATP binding cassette transporters, which move them across the cell membrane. We have recently reported a crystal structure of the molybdate/tungstate binding protein ModA/WtpA from Archaeoglobus fulgidus, which revealed an octahedrally coordinated central metal atom. By contrast, the previously determined structures of three bacterial homologs showed tetracoordinate molybdenum and tungsten atoms in their binding pockets. Until then, coordination numbers above four had only been found for molybdenum/tungsten in metalloenzymes where these metal atoms are part of the catalytic cofactors and coordinated by mostly non-oxygen ligands. We now report a high-resolution structure of A. fulgidus ModA/WtpA, as well as crystal structures of four additional homologs, all bound to tungstate. These crystal structures match X-ray absorption spectroscopy measurements from soluble, tungstate-bound protein, and reveal the details of the distorted octahedral coordination. Our results demonstrate that the distorted octahedral geometry is not an exclusive feature of the A. fulgidus protein, and suggest distinct binding modes of the binding proteins from archaea and bacteria.
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Affiliation(s)
- Kaspar Hollenstein
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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29
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30
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Davidson AL, Dassa E, Orelle C, Chen J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 2008; 72:317-64, table of contents. [PMID: 18535149 PMCID: PMC2415747 DOI: 10.1128/mmbr.00031-07] [Citation(s) in RCA: 981] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.
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Affiliation(s)
- Amy L Davidson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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31
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Pordea A, Creus M, Panek J, Duboc C, Mathis D, Novic M, Ward TR. Artificial Metalloenzyme for Enantioselective Sulfoxidation Based on Vanadyl-Loaded Streptavidin. J Am Chem Soc 2008; 130:8085-8. [DOI: 10.1021/ja8017219] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anca Pordea
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Marc Creus
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Jaroslaw Panek
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Carole Duboc
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Déborah Mathis
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Marjana Novic
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | - Thomas R. Ward
- Institute of Chemistry, University of Neuchâtel, Avenue Bellevaux 51, CP 158,2009 Neuchâtel, Switzerland, Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, and Département de Chimie Moléculaire UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:393-9. [DOI: 10.1016/j.bbapap.2007.11.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 11/08/2007] [Accepted: 11/13/2007] [Indexed: 11/22/2022]
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Hollenstein K, Frei DC, Locher KP. Structure of an ABC transporter in complex with its binding protein. Nature 2007; 446:213-6. [PMID: 17322901 DOI: 10.1038/nature05626] [Citation(s) in RCA: 382] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 01/26/2007] [Indexed: 11/09/2022]
Abstract
ATP-binding cassette (ABC) transporter proteins carry diverse substrates across cell membranes. Whereas clinically relevant ABC exporters are implicated in various diseases or cause multidrug resistance of cancer cells, bacterial ABC importers are essential for the uptake of nutrients, including rare elements such as molybdenum. A detailed understanding of their mechanisms requires direct visualization at high resolution and in distinct conformations. Our recent structure of the multidrug ABC exporter Sav1866 has revealed an outward-facing conformation of the transmembrane domains coupled to a closed conformation of the nucleotide-binding domains, reflecting the ATP-bound state. Here we present the 3.1 A crystal structure of a putative molybdate transporter (ModB2C2) from Archaeoglobus fulgidus in complex with its binding protein (ModA). Twelve transmembrane helices of the ModB subunits provide an inward-facing conformation, with a closed gate near the external membrane boundary. The ATP-hydrolysing ModC subunits reveal a nucleotide-free, open conformation, whereas the attached binding protein aligns the substrate-binding cleft with the entrance to the presumed translocation pathway. Structural comparison of ModB2C2A with Sav1866 suggests a common alternating access and release mechanism, with binding of ATP promoting an outward-facing conformation and dissociation of the hydrolysis products promoting an inward-facing conformation.
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Affiliation(s)
- Kaspar Hollenstein
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
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34
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Koropatkin NM, Koppenaal DW, Pakrasi HB, Smith TJ. The structure of a cyanobacterial bicarbonate transport protein, CmpA. J Biol Chem 2006; 282:2606-14. [PMID: 17121816 DOI: 10.1074/jbc.m610222200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of the food chain by fixing carbon and nitrogen into cellular biomass. To compensate for the low selectivity of Rubisco for CO2 over O2, cyanobacteria have developed highly efficient CO2-concentrating machinery of which the ABC transport system CmpABCD from Synechocystis PCC 6803 is one component. Here, we have described the structure of the bicarbonate-binding protein CmpA in the absence and presence of bicarbonate and carbonic acid. CmpA is highly homologous to the nitrate transport protein NrtA. CmpA binds carbonic acid at the entrance to the ligand-binding pocket, whereas bicarbonate binds in nearly an identical location compared with nitrate binding to NrtA. Unexpectedly, bicarbonate binding is accompanied by a metal ion, identified as Ca2+ via inductively coupled plasma optical emission spectrometry. The binding of bicarbonate and metal appears to be highly cooperative and suggests that CmpA may co-transport bicarbonate and calcium or that calcium acts a cofactor in bicarbonate transport.
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35
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Bevers LE, Hagedoorn PL, Krijger GC, Hagen WR. Tungsten transport protein A (WtpA) in Pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. J Bacteriol 2006; 188:6498-505. [PMID: 16952940 PMCID: PMC1595483 DOI: 10.1128/jb.00548-06] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeon Pyrococcus furiosus. This tungstate transport protein A (WtpA) is part of a new ABC transporter system selective for tungstate and molybdate. WtpA has very low sequence similarity with the earlier-characterized transport proteins ModA for molybdate and TupA for tungstate. Its structural gene is present in the genome of numerous archaea and some bacteria. The identification of this new tungstate and molybdate binding protein clarifies the mechanism of tungstate and molybdate transport in organisms that lack the known uptake systems associated with the ModA and TupA proteins, like many archaea. The periplasmic protein of this ABC transporter, WtpA (PF0080), was cloned and expressed in Escherichia coli. Using isothermal titration calorimetry, WtpA was observed to bind tungstate (dissociation constant [K(D)] of 17 +/- 7 pM) and molybdate (K(D) of 11 +/- 5 nM) with a stoichiometry of 1.0 mol oxoanion per mole of protein. These low K(D) values indicate that WtpA has a higher affinity for tungstate than do ModA and TupA and an affinity for molybdate similar to that of ModA. A displacement titration of molybdate-saturated WtpA with tungstate showed that the tungstate effectively replaced the molybdate in the binding site of the protein.
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Affiliation(s)
- Loes E Bevers
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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36
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Balan A, Santacruz CP, Moutran A, Ferreira RCC, Medrano FJ, Pérez CA, Ramos CHI, Ferreira LCS. The molybdate-binding protein (ModA) of the plant pathogen Xanthomonas axonopodis pv. citri. Protein Expr Purif 2006; 50:215-22. [PMID: 16879982 DOI: 10.1016/j.pep.2006.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/13/2006] [Accepted: 06/17/2006] [Indexed: 10/24/2022]
Abstract
The modABC operon of phytopathogen Xanthomonas axonopodis pv. citri (X. citri) encodes a putative ABC transporter involved in the uptake of the molybdate and tungstate anions. Sequence analyses showed high similarity values of ModA orthologs found in X. campestris pv. campestris (X. campestris) and Escherichia coli. The X. citri modA gene was cloned in pET28a and the recombinant protein, expressed in the E. coli BL21 (DE3) strain, purified by immobilized metal affinity chromatography. The purified protein remained soluble and specifically bound molybdate and tungstate with K(d) 0.29+/-0.12 microM and 0.58+/-0.14 microM, respectively. Additionally binding of molybdate drastically enhanced the thermal stability of the recombinant ModA as compared to the apoprotein. This is the first characterization of a ModA ortholog expressed by a phytopathogen and represents an important tool for functional, biochemical and structural analyses of molybdate transport in Xanthomonas species.
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Affiliation(s)
- Andrea Balan
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP 05008-900, Brazil.
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37
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Koropatkin NM, Pakrasi HB, Smith TJ. Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity. Proc Natl Acad Sci U S A 2006; 103:9820-5. [PMID: 16777960 PMCID: PMC1502537 DOI: 10.1073/pnas.0602517103] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of all aquatic food chains by fixing carbon and nitrogen into cellular biomass. The single most important nutrient for photosynthesis and growth is nitrate, which is severely limiting in many aquatic environments particularly the open ocean. It is therefore not surprising that NrtA, the solute-binding component of the high-affinity nitrate ABC transporter, is the single-most abundant protein in the plasma membrane of these bacteria. Here, we describe the structure of a nitrate-specific receptor, NrtA from Synechocystis sp. PCC 6803, complexed with nitrate and determined to a resolution of 1.5 A. NrtA is significantly larger than other oxyanion-binding proteins, representing a previously uncharacterized class of transport proteins. From sequence alignments, the only other solute-binding protein in this class is CmpA, a bicarbonate-binding protein. Therefore, these organisms created a solute-binding protein for two of the most important nutrients: inorganic nitrogen and carbon. The electrostatic charge distribution of NrtA appears to force the protein off the membrane while the flexible tether facilitates the delivery of nitrate to the membrane pore. The structure not only details the determinants for nitrate selectivity in NrtA but also the bicarbonate specificity in CmpA. Nitrate and bicarbonate transport are regulated by the cytoplasmic proteins NrtC and CmpC, respectively. Interestingly, the residues lining the ligand binding pockets suggest that they both bind nitrate. This implies that the nitrogen and carbon uptake pathways are synchronized by intracellular nitrate and nitrite.
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Affiliation(s)
- Nicole M. Koropatkin
- *Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132; and
| | | | - Thomas J. Smith
- *Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132; and
- To whom correspondence should be addressed. E-mail:
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38
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Santacruz CP, Balan A, Ferreira LCS, Barbosa JARG. Crystallization, data collection and phasing of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:289-91. [PMID: 16511325 PMCID: PMC2197186 DOI: 10.1107/s1744309106003812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 01/31/2006] [Indexed: 11/10/2022]
Abstract
Xanthomonas axonopodis pv. citri ModA protein is the ABC periplasmic binding component responsible for the capture of molybdate. The protein was crystallized with sodium molybdate using the hanging-drop vapour-diffusion method in the presence of PEG or sulfate. X-ray diffraction data were collected to a maximum resolution of 1.7 A using synchrotron radiation. The crystal belongs to the orthorhombic space group C222(1), with unit-cell parameters a = 68.15, b = 172.14, c = 112.04 A. The crystal structure was solved by molecular-replacement methods and structure refinement is in progress.
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Affiliation(s)
- C. P. Santacruz
- Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil
| | - A. Balan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil
| | - L. C. S. Ferreira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil
| | - J. A. R. G. Barbosa
- Centro de Biologia Molecular e Estrutural (CeBiMe), Laboratório Nacional de Luz Síncrotron (LNLS), CP 6192, Campinas, SP 13084-971, Brazil
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39
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Masters SL, Howlett GJ, Pau RN. The molybdate binding protein Mop from Haemophilus influenzae--biochemical and thermodynamic characterisation. Arch Biochem Biophys 2005; 439:105-12. [PMID: 15946640 DOI: 10.1016/j.abb.2005.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Revised: 04/19/2005] [Accepted: 04/26/2005] [Indexed: 11/18/2022]
Abstract
The protein Mop from Haemophilus influenzae is a member of the molbindin family of proteins. Using isothermal titration calorimetry (ITC), Mop was observed to bind molybdate at two distinct sites with a stoichiometry of 8 mol molybdate per Mop hexamer. Six moles of molybdate bound endothermically at high affinity sites (K(a)=8.5 x 10(7)M(-1)), while 2 mol of molybdate bound exothermically at lower affinity sites (K(a)=3.7 x 10(7)M(-1)). Sulphate was also found to bind weakly at the higher affinity sites. ITC revealed that the affinity of molybdate binding to the endothermic site decreased with increasing pH and was accompanied by the transfer from the buffer to the protein of one proton per Mop monomer. These kinetic and thermodynamic results are interpreted with reference to molbindin crystal structures and data concerning molbindin binding affinities. Mop binds molybdate with high specificity, capacity, and affinity which indicates that Mop has a role as an intracellular molybdate binding protein involved in oxyanion homeostasis.
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Affiliation(s)
- Seth L Masters
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Vic. 3010, Australia.
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40
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Dudev T, Lim C. Oxyanion Selectivity in Sulfate and Molybdate Transport Proteins: An ab Initio/CDM Study. J Am Chem Soc 2004; 126:10296-305. [PMID: 15315443 DOI: 10.1021/ja047951n] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A striking feature of sulfate (SO(4)(2-)) and molybdate (MoO(4)(2-)) transport proteins, such as SBP and ModA, which specifically bind SO(4)(2-) and MoO(4)(2-), respectively, is their ability to discriminate very similar anions with the same net charge, geometry, and hydrogen-bonding properties. Here, we determine to what extent (1) oxyanion-solvent interactions, (2) oxyanion-amino acid interactions, and (3) the anion-binding pocket sizes of the cognate protein contribute to the anion selectivity process in SO(4)(2-) and MoO(4)(2-) transport proteins by computing the free energies for replacing SO(4)(2-) with MoO(4)(2)(-)/WO(4)(2-) in model SO(4)(2-)-binding sites of varying degrees of solvent exposure using a combined quantum mechanical/continuum dielectric approach. The calculations reveal that MoO(4)(2-) transport proteins, such as ModA, specifically bind MoO(4)(2-)/WO(4)(2-) but not SO(4)(2-), mainly because the desolvation penalty of MoO(4)(2-)/WO(4)(2-) is significantly less than that of SO(4)(2-) and, to a lesser extent, because the large and rigid cavity in these proteins attenuates ligand interactions with SO(4)(2-), as compared to MoO(4)(2-). On the other hand, SO(4)(2-) transport proteins prefer SO(4)(2-) to MoO(4)(2-)/WO(4)(2-) because the small anion-binding pocket characteristic of these proteins inhibits binding of the larger MoO(4)(2-) and WO(4)(2-) anions. The calculations also help to explain the absence of positively charged Lys/Arg side chains in the anion-binding sites of SBP and ModA. During evolution, these transport proteins may have excluded cationic ligands from their binding sites because, on one hand, Lys/Arg do not contribute to the selectivity of the binding pocket and, on the other, they substantially stabilize the complex between the oxyanion and protein ligands, which in turn would prohibit the rapid release of the bound oxyanion at a certain stage during the transport process.
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Affiliation(s)
- Todor Dudev
- Contribution from the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, R.O.C
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41
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Zahalak M, Pratte B, Werth KJ, Thiel T. Molybdate transport and its effect on nitrogen utilization in the cyanobacterium Anabaena variabilis ATCC 29413. Mol Microbiol 2004; 51:539-49. [PMID: 14756792 DOI: 10.1046/j.1365-2958.2003.03851.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Molybdenum is an essential component of the cofactors of many metalloenzymes including nitrate reductase and Mo-nitrogenase. The cyanobacterium Anabaena variabilis ATCC 29413 uses nitrate and atmospheric N2 as sources of nitrogen for growth. Two of the three nitrogenases in this strain are Mo-dependent enzymes, as is nitrate reductase; thus, transport of molybdate is important for growth of this strain. High-affinity transport of molybdate in A. variabilis was mediated by an ABC-type transport system encoded by the products of modA and modBC. The modBC gene comprised a fused orf including components corresponding to modB and modC of Escherichia coli. The deduced ModC part of the fused gene lacked a recognizable molybdate-binding domain. Expression of modA and modBC was induced by starvation for molybdate. Mutants in modA or modBC were unable to grow using nitrate or Mo-nitrogenase. Growth using the alternative V-nitrogenase was not impaired in the mutants. A high concentration of molybdate (10 microM) supported normal growth of the modBC mutant using the Nif1 Mo-nitrogenase, indicating that there was a low-affinity molybdate transport system in this strain. The modBC mutant did not detectably transport low concentrations of 99Mo (molybdate), but did transport high concentrations. However, such transport was observed only after cells were starved for sulphate, suggesting that an inducible sulphate transport system might also serve as a low-affinity molybdate transport system in this strain.
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Affiliation(s)
- Marta Zahalak
- Department of Biology, University of Missouri-St Louis, 8001 Natural Bridge Road, St Louis, MO 63121-4499, USA
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42
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Heddle J, Scott DJ, Unzai S, Park SY, Tame JRH. Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli. J Biol Chem 2003; 278:50322-9. [PMID: 12960164 DOI: 10.1074/jbc.m307941200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria have evolved a number of tightly controlled import and export systems to maintain intracellular levels of the essential but potentially toxic metal nickel. Nickel homeostasis systems include the dedicated nickel uptake system nik found in Escherichia coli, a member of the ABC family of transporters, that involves a periplasmic nickel-binding protein, NikA. This is the initial nickel receptor and mediator of the chemotactic response away from nickel. We have solved the crystal structure of NikA protein in the presence and absence of nickel, showing that it behaves as a "classical" periplasmic binding protein. In contrast to other binding proteins, however, the ligand remains accessible to the solvent and is not completely enclosed. No direct bonds are formed between the metal cation and the protein. The nickel binding site is apolar, quite unlike any previously characterized protein nickel binding site. Despite relatively weak binding, NikA is specific for nickel. Using isothermal titration calorimetry, the dissociation constant for nickel was found to be approximately 10 microm and that for cobalt was approximately 20 times higher.
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Affiliation(s)
- Jonathan Heddle
- Protein Design Laboratory, Yokohama City University, Tsurumi, Suehiro 1-7-29, Yokohama 230-0045, Japan
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43
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Vyas NK, Vyas MN, Quiocho FA. Crystal structure of M tuberculosis ABC phosphate transport receptor: specificity and charge compensation dominated by ion-dipole interactions. Structure 2003; 11:765-74. [PMID: 12842040 DOI: 10.1016/s0969-2126(03)00109-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The 2.16 A structure of the phosphate-bound PstS-1, the primary extracellular receptor for the ABC phosphate transporter and immunodominant species-specific antigen of Mycobacterium tuberculosis, has been determined. The phosphate, completely engulfed in the cleft between two domains, is bound by 13 hydrogen bonds, 11 of which are formed with NH and OH dipolar donor groups. The further presence of two acidic residues, which serve as acceptors of the protonated phosphate, is key to conferring stringent specificity. The ion-dipole interactions between the phosphate and dipolar groups compensate the ligand's isolated negative charges. Moreover, the surprise finding that the electrostatic surface in and around the cleft is intensely negative demonstrates the power of ion-dipole interactions in anion binding and electrostatic balance. Additional functional features include both the flexible N-terminal segment that tethers PstS-1 on the cell surface and the hinge between the two domains, which should facilitate snaring the phosphate in the medium.
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Affiliation(s)
- Nand K Vyas
- Verna and Marrs McLean Department, Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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44
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Schrag JD, Huang W, Sivaraman J, Smith C, Plamondon J, Larocque R, Matte A, Cygler M. The crystal structure of Escherichia coli MoeA, a protein from the molybdopterin synthesis pathway. J Mol Biol 2001; 310:419-31. [PMID: 11428898 DOI: 10.1006/jmbi.2001.4771] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MoeA is involved in synthesis of the molybdopterin cofactor, although its function is not yet clearly defined. The three-dimensional structure of the Escherichia coli protein was solved at 2.2 A resolution. The locations of highly conserved residues among the prokaryotic and eukaryotic MoeA homologs identifies a cleft in the dimer interface as the likely functional site. Of the four domains of MoeA, domain 2 displays a novel fold and domains 1 and 4 each have only one known structural homolog. Domain 3, in contrast, is structurally similar to many other proteins. The protein that resembles domain 3 most closely is MogA, another protein required for molybdopterin cofactor synthesis. The overall similarity between MoeA and MogA, and the similarities in a constellation of residues that are strongly conserved in MoeA, suggests that these proteins bind similar ligands or substrates and may have similar functions.
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Affiliation(s)
- J D Schrag
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, PQ, Canada.
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45
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Makdessi K, Andreesen JR, Pich A. Tungstate Uptake by a highly specific ABC transporter in Eubacterium acidaminophilum. J Biol Chem 2001; 276:24557-64. [PMID: 11292832 DOI: 10.1074/jbc.m101293200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Gram-positive anaerobe Eubacterium acidaminophilum contains at least two tungsten-dependent enzymes: viologen-dependent formate dehydrogenase and aldehyde dehydrogenase. (185)W-Labeled tungstate was taken up by this organism with a maximum rate of 0.53 pmol min(-)1 mg(-)1 of protein at 36 degrees C. The uptake was not affected by equimolar amounts of molybdate. The genes tupABC coding for an ABC transporter specific for tungstate were cloned in the downstream region of genes encoding a tungsten-containing formate dehydrogenase. The substrate-binding protein, TupA, of this putative transporter was overexpressed in Escherichia coli, and its binding properties toward oxyanions were determined by a native polyacrylamide gel retardation assay. Only tungstate induced a shift of TupA mobility, suggesting that only this anion was specifically bound by TupA. If molybdate and sulfate were added in high molar excess (>1000-fold), they were also slightly bound by TupA. The K(d) value for tungstate was determined to be 0.5 microm. The genes encoding the tungstate-specific ABC transporter exhibited highest similarities to putative transporters from Methanobacterium thermoautotrophicum, Haloferax volcanii, Vibrio cholerae, and Campylobacter jejuni. These five transporters represent a separate phylogenetic group of oxyanion ABC transporters as evident from analysis of the deduced amino acid sequences of the binding proteins. Downstream of the tupABC genes, the genes moeA, moeA-1, moaA, and a truncated moaC have been identified by sequence comparison of the deduced amino acid sequences. They should participate in the biosynthesis of the pterin cofactor that is present in molybdenum- and tungsten-containing enzymes except nitrogenase.
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Affiliation(s)
- K Makdessi
- Institut für Mikrobiologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle, Germany
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46
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Gourley DG, Schuttelkopf AW, Anderson LA, Price NC, Boxer DH, Hunter WN. Oxyanion binding alters conformation and quaternary structure of the c-terminal domain of the transcriptional regulator mode. Implications for molybdate-dependent regulation, signaling, storage, and transport. J Biol Chem 2001; 276:20641-7. [PMID: 11259434 DOI: 10.1074/jbc.m100919200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molybdate-dependent transcriptional regulator ModE of Escherichia coli functions as a sensor of intracellular molybdate concentration and a regulator for the transcription of several operons that control the uptake and utilization of molybdenum. We present two high-resolution crystal structures of the C-terminal oxyanion-binding domain in complex with molybdate and tungstate. The ligands bind between subunits at the dimerization interface, and analysis reveals that oxyanion selectivity is determined primarily by size. The relevance of the structures is indicated by fluorescence measurements, which show that the oxyanion binding properties of the C-terminal domain of ModE are similar to those of the full-length protein. Comparisons with the apoprotein structure have identified structural rearrangements that occur on binding oxyanion. This molybdate-dependent conformational switch promotes a change in shape and alterations to the surface of the protein and may provide the signal for recruitment of other proteins to construct the machinery for transcription. Sequence and structure-based comparisons lead to a classification of molybdate-binding proteins.
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Affiliation(s)
- D G Gourley
- Wellcome Trust Biocentre, University of Dundee, Dundee, DD1 5EH, United Kingdom
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Delarbre L, Stevenson CE, White DJ, Mitchenall LA, Pau RN, Lawson DM. Two crystal structures of the cytoplasmic molybdate-binding protein ModG suggest a novel cooperative binding mechanism and provide insights into ligand-binding specificity. J Mol Biol 2001; 308:1063-79. [PMID: 11352591 DOI: 10.1006/jmbi.2001.4636] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The X-ray structures of the cytoplasmic molybdate-binding protein ModG from Azotobacter vinelandii in two different crystal forms have been determined. For such a small protein it is remarkably complex. Each 14.3 kDa subunit contains two small beta-barrel domains, which display an OB-fold motif, also seen in the related structure of ModE, a molybdenum-dependent transcriptional regulator, and very recently in the Mop protein that, like ModG, has been implicated in molybdenum homeostasis within the cell. In contrast to earlier speculation, the functional unit of ModG is actually not a dimer (as in ModE), but a trimer capable of binding a total of eight molybdate molecules that are distributed between two disparate types of site. All the binding sites are located at subunit interfaces, with one type lying on a crystallographic 3-fold axis, whilst the other lies between pairs of subunits. The two types of site are linked by short hydrogen bond networks that may suggest a cooperative binding mechanism. A superposition of two subunits of the ModG trimer on the apo-ModE dimer allows the probable locations of the molybdate-binding sites of the latter to be assigned. Through structural comparisons with other oxyanion-binding proteins, including Mop and ModE, it is possible to speculate about ligand-binding affinities, selectivity and evolution.
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Affiliation(s)
- L Delarbre
- Department of Biological Chemistry, Norwich, NR4 7UH, UK
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Abstract
In both bacteria and archaea, molybdate is transported by an ABC-type transporter comprising three proteins, ModA (periplasmic binding protein), ModB (membrane protein) and ModC, the ATPase. The modABC operon expression is controlled by ModE-Mo. In the absence of the high-affinity molybdate transporter, molybdate is also transported by another ABC transporter which transports sulfate/thiosulfate as well as by a nonspecific anion transporter. Comparative analysis of the molybdate transport proteins in various bacteria and archaea is the focus of this review.
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Affiliation(s)
- W T Self
- NHLBI, NIH, Bethesda, MD 20892, USA
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Wagner UG, Stupperich E, Kratky C. Structure of the molybdate/tungstate binding protein mop from Sporomusa ovata. Structure 2000; 8:1127-36. [PMID: 11080635 DOI: 10.1016/s0969-2126(00)00525-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Transport of molybdenum into bacteria involves a high-affinity ABC transporter system whose expression is controlled by a repressor protein called ModE. While molybdate transport is tightly coupled to utilization in some bacteria, other organisms have molybdenum storage proteins. One class of putative molybdate storage proteins is characterized by a sequence consisting of about 70 amino acids (Mop). A tandem repeat of Mop sequences also constitutes the molybdate binding domain of ModE. RESULTS We have determined the crystal structure of the 7 kDa Mop protein from the methanol-utilizing anaerobic eubacterium Sporomusa ovata grown in the presence of molybdate and tungstate. The protein occurs as highly symmetric hexamers binding eight oxyanions. Each peptide assumes a so-called OB fold, which has previously also been observed in ModE. There are two types of oxyanion binding sites in Mo at the interface between two or three peptides. All oxyanion binding sites were found to be occupied by WO(4) rather than MoO(4). CONCLUSIONS The biological function of proteins containing only Mop sequences is unknown, but they have been implicated in molybdate homeostasis and molybdopterin cofactor biosynthesis. While there are few indications that the S. ovata Mop binds pterin, the structure suggests that only the type-1 oxyanion binding sites would be sufficiently accessible to bind a cofactor. The observed occupation of the oxyanion binding sites by WO(4) indicates that Mop might also be involved in controlling intracellular tungstate levels.
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Affiliation(s)
- U G Wagner
- Institut für Chemie Strukturbiologie Karl-Franzens-Universität A-8010, Graz, Austria
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Quillin ML, Breyer WA, Griswold IJ, Matthews BW. Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme. J Mol Biol 2000; 302:955-77. [PMID: 10993735 DOI: 10.1006/jmbi.2000.4063] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the relative importance of size and polarizability in ligand binding within proteins, we have determined the crystal structures of pseudo wild-type and cavity-containing mutant phage T4 lysozymes in the presence of argon, krypton, and xenon. These proteins provide a representative sample of predominantly apolar cavities of varying size and shape. Even though the volumes of these cavities range up to the equivalent of five xenon atoms, the noble gases bind preferentially at highly localized sites that appear to be defined by constrictions in the walls of the cavities, coupled with the relatively large radii of the noble gases. The cavities within pseudo wild-type and L121A lysozymes each bind only a single atom of noble gas, while the cavities within mutants L133A and F153A have two independent binding sites, and the L99A cavity has three interacting sites. The binding of noble gases within two double mutants was studied to characterize the additivity of binding at such sites. In general, when a cavity in a protein is created by a "large-to-small" substitution, the surrounding residues relax somewhat to reduce the volume of the cavity. The binding of xenon and, to a lesser degree, krypton and argon, tend to expand the volume of the cavity and to return it closer to what it would have been had no relaxation occurred. In nearly all cases, the extent of binding of the noble gases follows the trend xenon>krypton>argon. Pressure titrations of the L99A mutant have confirmed that the crystallographic occupancies accurately reflect fractional saturation of the binding sites. The trend in noble gas affinity can be understood in terms of the effects of size and polarizability on the intermolecular potential. The plasticity of the protein matrix permits repulsion due to increased ligand size to be more than compensated for by attraction due to increased ligand polarizability. These results have implications for the mechanism of general anesthesia, the migration of small ligands within proteins, the detection of water molecules within apolar cavities and the determination of crystallographic phases.
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Affiliation(s)
- M L Quillin
- Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR, 97403, USA
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