Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae

Valencia, Daniel W.; Meléndez, Ady B.; Melendrez, Isaac A.; Yukl, Erik T.

doi:10.3390/ijms24010548

Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae

Journal Article · Thu Dec 29 00:00:00 EST 2022 · International Journal of Molecular Sciences (Online)

DOI:https://doi.org/10.3390/ijms24010548· OSTI ID:2471006

Valencia, Daniel W. ^[1]; Meléndez, Ady B. ^[1]; Melendrez, Isaac A. ^[1]; ^[1]

New Mexico State Univ., Las Cruces, NM (United States)

ATP binding cassette (ABC) transporters are the primary means by which bacteria acquire trace elements from the environment. They rely on solute binding proteins (SBPs) to bind the relevant substrate and deliver it to the integral membrane permease for ATP-powered import into the cytoplasm. SBPs of cluster A-I are known to facilitate the transport of essential metals zinc, manganese, and iron, and many have been characterized to date. A group of ABC transporter operons dubbed zinc-regulated genes (zrg) have recently been shown to transport zinc with putative SBPs (zrgA) bearing no homology to the classical cluster A-I family, and a recent crystal structure of a representative protein from Pseudomonas aeruginosa shows no structural similarity to classical SBPs. Thus, the ZrgA proteins appear to represent a newly discovered family of zinc SBPs widespread among Gram-negative bacteria, including human pathogens. Here, we have determined the crystal structure of ZrgA from Vibrio cholerae and characterized its zinc binding in vitro and function in vivo. We also assessed the role of a histidine-rich sequence that appears to be a hallmark of ZrgA proteins that is particularly long in V. cholerae ZrgA. The results show that the zrgA gene is critical to the function of the operon, consistent with a function as an SBP in this system. Further, the His-rich region is not essential to the function of ZrgA, but it does provide additional zinc binding sites in vitro. The structure and zinc binding data for ZrgA reveal interesting differences between it and its homologue from P. aeruginosa, illustrating diversity within this little-studied protein family.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2471006

Journal Information:: International Journal of Molecular Sciences (Online), Journal Name: International Journal of Molecular Sciences (Online) Journal Issue: 1 Vol. 24; ISSN 1422-0067

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

References (48)

An updated structural classification of substrate-binding proteins Scheepers, Giel H.; Lycklama a. Nijeholt, Jelger A.; Poolman, Bert FEBS Letters, Vol. 590, Issue 23 https://doi.org/10.1002/1873-3468.12445	journal	October 2016
Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase Kuzmič, Petr Analytical Biochemistry, Vol. 237, Issue 2 https://doi.org/10.1006/abio.1996.0238	journal	June 1996
Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli Yatsunyk, Liliya A.; Easton, J. Allen; Kim, Lydia R. JBIC Journal of Biological Inorganic Chemistry, Vol. 13, Issue 2 https://doi.org/10.1007/s00775-007-0320-0	journal	November 2007
A deliberate approach to screening for initial crystallization conditions of biological macromolecules Luft, Joseph R.; Collins, Robert J.; Fehrman, Nancy A. Journal of Structural Biology, Vol. 142, Issue 1 https://doi.org/10.1016/S1047-8477(03)00048-0	journal	April 2003
The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc Ilari, Andrea; Alaleona, Flaminia; Tria, Giancarlo Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1840, Issue 1 https://doi.org/10.1016/j.bbagen.2013.10.010	journal	January 2014
Nutritional immunity beyond iron: a role for manganese and zinc Kehl-Fie, Thomas E.; Skaar, Eric P. Current Opinion in Chemical Biology, Vol. 14, Issue 2 https://doi.org/10.1016/j.cbpa.2009.11.008	journal	April 2010
A structural classification of substrate-binding proteins Berntsson, Ronnie P. -A.; Smits, Sander H. J.; Schmitt, Lutz FEBS Letters, Vol. 584, Issue 12 https://doi.org/10.1016/j.febslet.2010.04.043	journal	April 2010
Structural and functional characterizations of the C-terminal domains of CzcD proteins Udagedara, Saumya R.; La Porta, Daniel M.; Spehar, Christian Journal of Inorganic Biochemistry, Vol. 208 https://doi.org/10.1016/j.jinorgbio.2020.111087	journal	July 2020
Alternating Access in Maltose Transporter Mediated by Rigid-Body Rotations Khare, Dheeraj; Oldham, Michael L.; Orelle, Cedric Molecular Cell, Vol. 33, Issue 4 https://doi.org/10.1016/j.molcel.2009.01.035	journal	February 2009
Two ABC Transporters and a Periplasmic Metallochaperone Participate in Zinc Acquisition in Paracoccus denitrificans Neupane, Durga P.; Kumar, Santosh; Yukl, Erik T. Biochemistry, Vol. 58, Issue 2 https://doi.org/10.1021/acs.biochem.8b00854	journal	October 2018
Spectroscopic Determination of Tryptophan and Tyrosine in Proteins ^* Edelhoch, Harold Biochemistry, Vol. 6, Issue 7 https://doi.org/10.1021/bi00859a010	journal	July 1967
MauG, a Novel Diheme Protein Required for Tryptophan Tryptophylquinone Biogenesis ^† Wang, Yongting; Graichen, M. Elizabeth; Liu, Aimin Biochemistry, Vol. 42, Issue 24 https://doi.org/10.1021/bi034243q	journal	June 2003
Metal Binding Studies and EPR Spectroscopy of the Manganese Transport Regulator MntR ^† Golynskiy, Misha V.; Gunderson, William A.; Hendrich, Michael P. Biochemistry, Vol. 45, Issue 51 https://doi.org/10.1021/bi0607406	journal	December 2006
Possible Regulatory Role for the Histidine-Rich Loop in the Zinc Transport Protein, ZnuA ^† ^, ^‡ Wei, Baoxian; Randich, Amelia M.; Bhattacharyya-Pakrasi, Maitrayee Biochemistry, Vol. 46, Issue 30 https://doi.org/10.1021/bi700763w	journal	July 2007
Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan Nature Methods, Vol. 6, Issue 5, p. 343-345 https://doi.org/10.1038/nmeth.1318	journal	April 2009
SignalP 4.0: discriminating signal peptides from transmembrane regions Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar Nature Methods, Vol. 8, Issue 10 https://doi.org/10.1038/nmeth.1701	journal	September 2011
Fiji: an open-source platform for biological-image analysis Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2019	journal	June 2012
SignalP 5.0 improves signal peptide predictions using deep neural networks Almagro Armenteros, José Juan; Tsirigos, Konstantinos D.; Sønderby, Casper Kaae Nature Biotechnology, Vol. 37, Issue 4 https://doi.org/10.1038/s41587-019-0036-z	journal	February 2019
ZnuA and zinc homeostasis in Pseudomonas aeruginosa Pederick, Victoria G.; Eijkelkamp, Bart A.; Begg, Stephanie L. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep13139	journal	August 2015
Advances in the molecular understanding of biological zinc transport Blindauer, Claudia A. Chemical Communications, Vol. 51, Issue 22 https://doi.org/10.1039/C4CC10174J	journal	January 2015
Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen Staphylococcus pseudintermedius Abate, Francesca; Malito, Enrico; Cozzi, Roberta Bioscience Reports, Vol. 34, Issue 6 https://doi.org/10.1042/BSR20140088	journal	November 2014
Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily Crow, Allister; Greene, Nicholas P.; Kaplan, Elise Proceedings of the National Academy of Sciences, Vol. 114, Issue 47 https://doi.org/10.1073/pnas.1712153114	journal	November 2017
Identification of the Key Protein for Zinc Uptake in Hemophilus influenzae Lu, Desheng; Boyd, Beth; Lingwood, Clifford A. Journal of Biological Chemistry, Vol. 272, Issue 46 https://doi.org/10.1074/jbc.272.46.29033	journal	November 1997
Transcriptional Regulation, Metal Binding Properties and Structure of Pden1597, an Unusual Zinc Transport Protein from Paracoccus denitrificans Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu Journal of Biological Chemistry, Vol. 290, Issue 19 https://doi.org/10.1074/jbc.M115.645853	journal	March 2015
AztD, a Periplasmic Zinc Metallochaperone to an ATP-binding Cassette (ABC) Transporter System in Paracoccus denitrificans Handali, Melody; Roychowdhury, Hridindu; Neupane, Durga P. Journal of Biological Chemistry, Vol. 290, Issue 50 https://doi.org/10.1074/jbc.M115.684506	journal	October 2015
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
ABC transporters: one, two or four extracytoplasmic substrate-binding sites? van der Heide, T.; Poolman, B. EMBO reports, Vol. 3, Issue 10 https://doi.org/10.1093/embo-reports/kvf201	journal	October 2002
UniProt: a worldwide hub of protein knowledge Consortium, The UniProt Nucleic Acids Research https://doi.org/10.1093/nar/gky1049		November 2018
The EMBL-EBI search and sequence analysis tools APIs in 2019 Madeira, Fábio; Park, Young mi; Lee, Joon Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz268	journal	April 2019
Emerging Aeromonas Species Infections and Their Significance in Public Health Igbinosa, Isoken H.; Igumbor, Ehimario U.; Aghdasi, Farhad The Scientific World Journal, Vol. 2012 https://doi.org/10.1100/2012/625023	journal	January 2012
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking byPseudomonas aeruginosa Fiorillo, Annarita; Battistoni, Andrea; Ammendola, Serena Acta Crystallographica Section D Structural Biology, Vol. 77, Issue 11 https://doi.org/10.1107/S2059798321009608	journal	October 2021
The general transition metal (Tro) and Zn ²⁺ (Znu) transporters in Treponema pallidum : analysis of metal specificities and expression profiles Desrosiers, Daniel C.; Sun, Yong Cheng; Zaidi, Akbar A. Molecular Microbiology, Vol. 65, Issue 1 https://doi.org/10.1111/j.1365-2958.2007.05771.x	journal	July 2007
AdcA and AdcAII employ distinct zinc acquisition mechanisms and contribute additively to zinc homeostasis in S treptococcus pneumoniae: AdcA and pneumococcal zinc homeostasis Plumptre, Charles D.; Eijkelkamp, Bart A.; Morey, Jacqueline R. Molecular Microbiology, Vol. 91, Issue 4 https://doi.org/10.1111/mmi.12504	journal	January 2014
The structural basis of bacterial manganese import Neville, Stephanie L.; Sjöhamn, Jennie; Watts, Jacinta A. Science Advances, Vol. 7, Issue 32 https://doi.org/10.1126/sciadv.abg3980	journal	August 2021
Dual Zinc Transporter Systems in Vibrio cholerae Promote Competitive Advantages over Gut Microbiome Sheng, Ying; Fan, Fenxia; Jensen, Owen Infection and Immunity, Vol. 83, Issue 10 https://doi.org/10.1128/IAI.00447-15	journal	October 2015
MacAB Is Involved in the Secretion of Escherichia coli Heat-Stable Enterotoxin II Yamanaka, H.; Kobayashi, H.; Takahashi, E. Journal of Bacteriology, Vol. 190, Issue 23 https://doi.org/10.1128/JB.00853-08	journal	September 2008
Identification and Characterization of RbmA, a Novel Protein Required for the Development of Rugose Colony Morphology and Biofilm Structure in Vibrio cholerae Fong, Jiunn C. N.; Karplus, Kevin; Schoolnik, Gary K. Journal of Bacteriology, Vol. 188, Issue 3 https://doi.org/10.1128/JB.188.3.1049-1059.2006	journal	February 2006
Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems Davidson, A. L.; Dassa, E.; Orelle, C. Microbiology and Molecular Biology Reviews, Vol. 72, Issue 2 https://doi.org/10.1128/MMBR.00031-07	journal	June 2008
ABC Transporters: From Microorganisms to Man Higgins, C. F. Annual Review of Cell Biology, Vol. 8, Issue 1 https://doi.org/10.1146/annurev.cb.08.110192.000435	journal	November 1992
Structural Features Mediating Zinc Binding and Transfer in the AztABCD Zinc Transporter System Meni, Anusha; Yukl, Erik T. Biomolecules, Vol. 10, Issue 8 https://doi.org/10.3390/biom10081156	journal	August 2020
Specificity of Interactions between Components of Two Zinc ABC Transporters in Paracoccus denitrificans Meléndez, Ady Berenice; Valencia, Daniel; Yukl, Erik Thomas International Journal of Molecular Sciences, Vol. 21, Issue 23 https://doi.org/10.3390/ijms21239098	journal	November 2020

Similar Records

Crystal Structure of VC0702 at 2.0 angstrom: A Conserved Hypothetical Protein from Vibrio Cholerae

Journal Article · Thu Jun 01 00:00:00 EDT 2006 · Proteins. Structure, Function, and Bioinformatics · OSTI ID:889041

Crystal Structure of VC0702 at 2.0 Angstrom: Conserved Hypothetical Protein from Vibrio Cholerae

Journal Article · Sat Dec 31 23:00:00 EST 2005 · Proteins: Struc. Func. Bioinformatics · OSTI ID:914149

Transcriptional regulation, metal binding properties and structure of Pden1597, an unusual zinc transport protein from Paracoccus denitrificans

Journal Article · Tue Mar 17 20:00:00 EDT 2015 · Journal of Biological Chemistry · OSTI ID:1347699

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ABC transporters
solute-binding protein
zinc

Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae

Citation Formats

References (48)

Similar Records

Related Subjects