The YbeY Protein from Escherichia Coli is a Metalloprotein

Overview

Journal Acta Crystallogr Sect F Struct Biol Cryst Commun

Date 2006 Mar 3

PMID 16511207

Citations 30

Authors

Chenyang Zhan

Elena V Fedorov

WuXian Shi

U A Ramagopal

R Thirumuruhan

Babu A Manjasetty

Steve C Almo

Andras Fiser

Mark R Chance

Alexander A Fedorov

Affiliations

Soon will be listed here.

Abstract

The three-dimensional crystallographic structure of the ybeY protein from Escherichia coli (SwissProt entry P77385) is reported at 2.7 A resolution. YbeY is a hypothetical protein that belongs to the UPF0054 family. The structure reveals that the protein binds a metal ion in a tetrahedral geometry. Three coordination sites are provided by histidine residues, while the fourth might be a water molecule that is not seen in the diffraction map because of its relatively low resolution. X-ray fluorescence analysis of the purified protein suggests that the metal is a nickel ion. The structure of ybeY and its sequence similarity to a number of predicted metal-dependent hydrolases provides a functional assignment for this protein family. The figures and tables of this paper were prepared using semi-automated tools, termed the Autopublish server, developed by the New York Structural GenomiX Research Consortium, with the goal of facilitating the rapid publication of crystallographic structures that emanate from worldwide Structural Genomics efforts, including the NIH-funded Protein Structure Initiative.

Citing Articles

Crystal Structure of the Metallo-Endoribonuclease YbeY from .

Lee J, Jo I, Kwon A, Ha N J Microbiol Biotechnol. 2022; 33(1):28-34.

PMID: 36457189 PMC: 9895993. DOI: 10.4014/jmb.2209.09019.

A Mutant Era GTPase Suppresses Phenotypes Caused by Loss of Highly Conserved YbeY Protein in .

Babu V, Sankari S, Ghosal A, Walker G Front Microbiol. 2022; 13:896075.

PMID: 35663862 PMC: 9159920. DOI: 10.3389/fmicb.2022.896075.

The world of ribonucleases from pseudomonads: a short trip through the main features and singularities.

Apura P, Goncalves L, Viegas S, Arraiano C Microb Biotechnol. 2021; 14(6):2316-2333.

PMID: 34427985 PMC: 8601179. DOI: 10.1111/1751-7915.13890.

Functional Genomic Analyses of the 21q22.3 Locus Identifying Functional Variants and Candidate Gene for Breast Cancer Risk.

Shidal C, Shu X, Wu J, Wang J, Huang S, Long J Cancers (Basel). 2021; 13(9).

PMID: 33922500 PMC: 8122893. DOI: 10.3390/cancers13092037.

YbeY controls the type III and type VI secretion systems and biofilm formation through RetS in .

Xia Y, Xu C, Wang D, Weng Y, Jin Y, Bai F Appl Environ Microbiol. 2020; 87(5).

PMID: 33310711 PMC: 8090875. DOI: 10.1128/AEM.02171-20.

References

Livingstone C, Barton G . Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci. 1993; 9(6):745-56. DOI: 10.1093/bioinformatics/9.6.745. View

Oganesyan V, Busso D, Brandsen J, Chen S, Jancarik J, Kim R . Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus. Acta Crystallogr D Biol Crystallogr. 2003; 59(Pt 7):1219-23. DOI: 10.1107/s0907444903011028. View

Barton G . ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 1993; 6(1):37-40. DOI: 10.1093/protein/6.1.37. View

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

Shi W, Zhan C, Ignatov A, Manjasetty B, Marinkovic N, Sullivan M . Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure. 2005; 13(10):1473-86. DOI: 10.1016/j.str.2005.07.014. View

Chance M, Fiser A, Sali A, Pieper U, Eswar N, Xu G . High-throughput computational and experimental techniques in structural genomics. Genome Res. 2004; 14(10B):2145-54. PMC: 528931. DOI: 10.1101/gr.2537904. View

Jones T, Zou J, Cowan S, Kjeldgaard M . Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991; 47 ( Pt 2):110-9. DOI: 10.1107/s0108767390010224. View

Tatusov R, Natale D, Garkavtsev I, Tatusova T, Shankavaram U, Rao B . The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2000; 29(1):22-8. PMC: 29819. DOI: 10.1093/nar/29.1.22. View

Holm L, Sander C . Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 1998; 26(1):316-9. PMC: 147193. DOI: 10.1093/nar/26.1.316. View

10.

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

11.

Terwilliger T, Berendzen J . Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 4):849-61. PMC: 2746121. DOI: 10.1107/s0907444999000839. View

12.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

13.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

14.

Henrick K, Thornton J . PQS: a protein quaternary structure file server. Trends Biochem Sci. 1998; 23(9):358-61. DOI: 10.1016/s0968-0004(98)01253-5. View

15.

Bateman A, Coin L, Durbin R, Finn R, Hollich V, Griffiths-Jones S . The Pfam protein families database. Nucleic Acids Res. 2003; 32(Database issue):D138-41. PMC: 308855. DOI: 10.1093/nar/gkh121. View

16.

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

17.

Terwilliger T . Reciprocal-space solvent flattening. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 11):1863-71. PMC: 2745881. DOI: 10.1107/s0907444999010033. View