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Nguyen HL, Crowhurst KA. Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:93-98. [PMID: 38642264 PMCID: PMC11192017 DOI: 10.1007/s12104-024-10173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Abstract
ModA is a soluble periplasmic molybdate-binding protein found in most gram-negative bacteria. It is part of the ABC transporter complex ModABC that moves molybdenum into the cytoplasm, to be used by enzymes that carry out various redox reactions. Since there is no clear analog for ModA in humans, this protein could be a good target for antibacterial drug design. Backbone 1H, 13C and 15N chemical shifts of apo and molybdate-bound ModA from E. coli were assigned at pHs 6.0 and 4.5. In addition, side chain atoms were assigned for apo ModA at pH 6.0. When comparing apo and molybdate-bound ModA at pH 6.0, large chemical shift perturbations are observed, not only in areas near the bound metal, but also in regions that are distant from the metal-binding site. Given the significant conformational change between apo and holo ModA, we might expect the large chemical shift changes to be more widespread; however, since they are limited to specific regions, the residues with large perturbations may reveal allosteric sites that could ultimately be important for the design of antibiotics that target ModA.
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Affiliation(s)
- Hiep Ld Nguyen
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA, 91330-8262, USA
| | - Karin A Crowhurst
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA, 91330-8262, USA.
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2
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Zhao Q, Su X, Wang Y, Liu R, Bartlam M. Structural analysis of molybdate binding protein ModA from Klebsiella pneumoniae. Biochem Biophys Res Commun 2023; 681:41-46. [PMID: 37751633 DOI: 10.1016/j.bbrc.2023.09.055] [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: 08/26/2023] [Accepted: 09/20/2023] [Indexed: 09/28/2023]
Abstract
Klebsiella pneumoniae, a facultative anaerobe, relies on acquiring molybdenum to sustain growth in anaerobic conditions, a crucial factor for the pathogen to establish infections within host environments. Molybdenum plays a critical role in pathogenesis as it forms an essential component of cofactors for molybdoenzymes. K. pneumoniae utilizes the ABC (ATP-Binding-Cassette) transporter encoded by the modABC operon for uptake of the group VI elements molybdenum and tungsten. In this study, we determined the X-ray crystal structures of both the molybdenum-free and molybdenum-bound substrate-binding protein (SBP) ModA from Klebsiella pneumoniae to 2.00 Å and 1.77 Å resolution respectively. ModA crystallizes in the space group P222 with a single monomer in one asymmetric unit. The purified protein remained soluble and specifically bound molybdate and tungstate with Kd values of 6.3 nM and 5.2 nM, respectively. Tungstate competes with molybdate by binding to ModA, resulting in enhanced antimicrobial activity. These data provide a starting point for structural and functional analyses of molybdate transport in K. pneumoniae.
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Affiliation(s)
- Qi Zhao
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xiaokang Su
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Yanan Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300071, China.
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Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220. Sci Rep 2022; 12:4805. [PMID: 35314715 PMCID: PMC8938411 DOI: 10.1038/s41598-022-08459-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Paradigms of metabolic strategies employed by photoautotrophic marine picocyanobacteria have been challenged in recent years. Based on genomic annotations, picocyanobacteria are predicted to assimilate organic nutrients via ATP-binding cassette importers, a process mediated by substrate-binding proteins. We report the functional characterisation of a modified sugar-binding protein, MsBP, from a marine Synechococcus strain, MITS9220. Ligand screening of MsBP shows a specific affinity for zinc (KD ~ 1.3 μM) and a preference for phosphate-modified sugars, such as fructose-1,6-biphosphate, in the presence of zinc (KD ~ 5.8 μM). Our crystal structures of apo MsBP (no zinc or substrate-bound) and Zn-MsBP (with zinc-bound) show that the presence of zinc induces structural differences, leading to a partially-closed substrate-binding cavity. The Zn-MsBP structure also sequesters several sulphate ions from the crystallisation condition, including two in the binding cleft, appropriately placed to mimic the orientation of adducts of a biphosphate hexose. Combined with a previously unseen positively charged binding cleft in our two structures and our binding affinity data, these observations highlight novel molecular variations on the sugar-binding SBP scaffold. Our findings lend further evidence to a proposed sugar acquisition mechanism in picocyanobacteria alluding to a mixotrophic strategy within these ubiquitous photosynthetic bacteria.
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Wang T, Du X, Ji L, Han Y, Dang J, Wen J, Wang Y, Pu Q, Wu M, Liang H. Pseudomonas aeruginosa T6SS-mediated molybdate transport contributes to bacterial competition during anaerobiosis. Cell Rep 2021; 35:108957. [PMID: 33852869 DOI: 10.1016/j.celrep.2021.108957] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/06/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022] Open
Abstract
Type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria and functions as a versatile protein export machinery that translocates effectors into eukaryotic or prokaryotic target cells. Growing evidence indicates that T6SS can deliver several effectors to promote bacterial survival in harmful environments through metal ion acquisition. Here, we report that the Pseudomonas aeruginosa H2-T6SS mediates molybdate (MoO42-) acquisition by secretion of a molybdate-binding protein, ModA. The expression of H2-T6SS genes is activated by the master regulator Anr and anaerobiosis. We also identified a ModA-binding protein, IcmP, an insulin-cleaving metalloproteinase outer membrane protein. The T6SS-ModA-IcmP system provides P. aeruginosa with a growth advantage in bacterial competition under anaerobic conditions and plays an important role in bacterial virulence. Overall, this study clarifies the role of T6SS in secretion of an anion-binding protein, emphasizing the fundamental importance of this bacterium using T6SS-mediated molybdate uptake to adapt to complex environmental conditions.
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Affiliation(s)
- Tietao Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Xiao Du
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Linxuan Ji
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Yuying Han
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Jing Dang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Jing Wen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Yarong Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China
| | - Qinqin Pu
- Department of Basic Science, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND 58203, USA
| | - Min Wu
- Department of Basic Science, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND 58203, USA
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi 710069, China.
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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: 1] [Impact Index Per Article: 0.3] [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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Radka CD, Labiuk SL, DeLucas LJ, Aller SG. Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms. Acta Crystallogr D Struct Biol 2019; 75:831-840. [PMID: 31478906 PMCID: PMC6719664 DOI: 10.1107/s2059798319010866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/02/2019] [Indexed: 12/23/2022] Open
Abstract
In the structural biology of bacterial substrate-binding proteins (SBPs), a growing number of comparisons between substrate-bound and substrate-free forms of metal atom-binding (cluster A-I) SBPs have revealed minimal structural differences between forms. These observations contrast with SBPs that bind substrates such as amino acids or nucleic acids and may undergo >60° rigid-body rotations. Substrate transfer in these SBPs is described by a Venus flytrap model, although this model may not apply to all SBPs. In this report, structures are presented of substrate-free (apo) and reconstituted substrate-bound (holo) YfeA, a polyspecific cluster A-I SBP from Yersinia pestis. It is demonstrated that an apo cluster A-I SBP can be purified by fractionation when co-expressed with its cognate transporter, adding an alternative strategy to the mutagenesis or biochemical treatment used to generate other apo cluster A-I SBPs. The apo YfeA structure contains 111 disordered protein atoms in a mobile helix located in the flexible carboxy-terminal lobe. Metal binding triggers a 15-fold reduction in the solvent-accessible surface area of the metal-binding site and reordering of the 111 protein atoms in the mobile helix. The flexible lobe undergoes a 13.6° rigid-body rotation that is driven by a spring-hammer metal-binding mechanism. This asymmetric rigid-body rotation may be unique to metal atom-binding SBPs (i.e. clusters A-I, A-II and D-IV).
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Affiliation(s)
- Christopher D. Radka
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shaunivan L. Labiuk
- Canadian Macromolecular Crystallography Facility, Canadian Light Source, Saskatoon, SK S7N 2V3, Canada
| | - Lawrence J. DeLucas
- Division of Human Exploration and Spaceflight, Aerospace Corporation, El Segundo, CA 90245, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, Birmingham, AL 35294, USA
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Rahman MM, Machuca MA, Roujeinikova A. Preliminary X-ray crystallographic studies on the Helicobacter pylori ABC transporter glutamine-binding protein GlnH. Drug Discov Ther 2019; 13:52-58. [DOI: 10.5582/ddt.2019.01008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mohammad M. Rahman
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
| | - Mayra A. Machuca
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
- Department of Biochemistry and Molecular Biology, Monash University
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Crystallisation and Preliminary Crystallographic Analysis of Helicobacter pylori Periplasmic Binding Protein YckK. CRYSTALS 2017. [DOI: 10.3390/cryst7110330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
AbstractABC transporters comprise a large, diverse, and ubiquitous superfamily of membrane active transporters. Their core architecture is a dimer of dimers, comprising two transmembrane (TM) domains that bind substrate, and two ATP-binding cassettes, which use the cell's energy currency to couple substrate translocation to ATP hydrolysis. Despite the availability of over a dozen resolved structures and a wealth of biochemical and biophysical data, this field is bedeviled by controversy and long-standing mechanistic questions remain unresolved. The prevailing paradigm for the ABC transport mechanism is the Switch Model, in which the ATP-binding cassettes dimerize upon binding two ATP molecules, and thence dissociate upon sequential ATP hydrolysis. This cycle of nucleotide-binding domain (NBD) dimerization and dissociation is coupled to a switch between inward- or outward facing conformations of a single TM channel; this alternating access enables substrate binding on one face of the membrane and its release at the other. Notwithstanding widespread acceptance of the Switch Model, there is substantial evidence that the NBDs do not separate very much, if at all, and thus physical separation of the ATP cassettes observed in crystallographic structures may be an artefact. An alternative Constant Contact Model has been proposed, in which ATP hydrolysis occurs alternately at the two ATP-binding sites, with one of the sites remaining closed and containing occluded nucleotide at all times. In this model, the cassettes remain in contact and the active sites swing open in an alternately seesawing motion. Whilst the concept of NBD association/dissociation in the Switch Model is naturally compatible with a single alternating-access channel, the asymmetric functioning proposed by the Constant Contact model suggests an alternating or reciprocating function in the TMDs. Here, a new model for the function of ABC transporters is proposed in which the sequence of ATP binding, hydrolysis, and product release in each active site is directly coupled to the analogous sequence of substrate binding, translocation and release in one of two functionally separate substrate translocation pathways. Each translocation pathway functions 180° out of phase. A wide and diverse selection of data for both ABC importers and exporters is examined, and the ability of the Switch and Reciprocating Models to explain the data is compared and contrasted. This analysis shows that not only can the Reciprocating Model readily explain the data; it also suggests straightforward explanations for the function of a number of atypical ABC transporters. This study represents the most coherent and complete attempt at an all-encompassing scheme to explain how these important proteins work, one that is consistent with sound biochemical and biophysical evidence.
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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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11
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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: 1.6] [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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Pietri R, Zerbs S, Corgliano DM, Allaire M, Collart FR, Miller LM. Biophysical and structural characterization of a sequence-diverse set of solute-binding proteins for aromatic compounds. J Biol Chem 2012; 287:23748-56. [PMID: 22577139 PMCID: PMC3390649 DOI: 10.1074/jbc.m112.352385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 04/21/2012] [Indexed: 12/20/2022] Open
Abstract
Rhodopseudomonas palustris metabolizes aromatic compounds derived from lignin degradation products and has the potential for bioremediation of xenobiotic compounds. We recently identified four possible solute-binding proteins in R. palustris that demonstrated binding to aromatic lignin monomers. Characterization of these proteins in the absence and presence of the aromatic ligands will provide unprecedented insights into the specificity and mode of aromatic ligand binding in solute-binding proteins. Here, we report the thermodynamic and structural properties of the proteins with aromatic ligands using isothermal titration calorimetry, small/wide angle x-ray scattering, and theoretical predictions. The proteins exhibit high affinity for the aromatic substrates with dissociation constants in the low micromolar to nanomolar range. The global shapes of the proteins are characterized by flexible ellipsoid-like structures with maximum dimensions in the 80-90-Å range. The data demonstrate that the global shapes remained unaltered in the presence of the aromatic ligands. However, local structural changes were detected in the presence of some ligands, as judged by the observed features in the wide angle x-ray scattering regime at q ~0.20-0.40 Å(-1). The theoretical models confirmed the elongated nature of the proteins and showed that they consist of two domains linked by a hinge. Evaluation of the protein-binding sites showed that the ligands were found in the hinge region and that ligand stabilization was primarily driven by hydrophobic interactions. Taken together, this study shows the capability of identifying solute-binding proteins that interact with lignin degradation products using high throughput genomic and biophysical approaches, which can be extended to other organisms.
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Affiliation(s)
- Ruth Pietri
- From the Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973 and
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | | | - Marc Allaire
- From the Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973 and
| | - Frank R. Collart
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Lisa M. Miller
- From the Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973 and
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