Structure of a Short-chain Dehydrogenase/reductase (SDR) Within a Genomic Island from a Clinical Strain of Acinetobacter Baumannii

Overview

Journal Acta Crystallogr F Struct Biol Commun

Specialty Chemistry

Date 2014 Oct 8

PMID 25286932

Citations 4

Authors

Bhumika S Shah

Sasha G Tetu

Stephen J Harrop

Ian T Paulsen

Bridget C Mabbutt

Affiliations

Soon will be listed here.

Abstract

Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.

Citing Articles

Crystallographic structure determination and analysis of a potential short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii.

Ghafoori S, Abdollahpour S, Shirmast P, Forwood J PLoS One. 2023; 18(8):e0289992.

PMID: 37616198 PMC: 10449147. DOI: 10.1371/journal.pone.0289992.

Microbial Proteins in Stomach Biopsies Associated with Gastritis, Ulcer, and Gastric Cancer.

Aziz S, Rasheed F, Akhter T, Zahra R, Konig S Molecules. 2022; 27(17).

PMID: 36080177 PMC: 9458002. DOI: 10.3390/molecules27175410.

Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases.

Cross E, Adams F, Waters J, Aragao D, Eijkelkamp B, Forwood J Sci Rep. 2021; 11(1):7050.

PMID: 33782435 PMC: 8007833. DOI: 10.1038/s41598-021-86400-1.

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii.

Shah B, Ashwood H, Harrop S, Farrugia D, Paulsen I, Mabbutt B PLoS One. 2018; 13(1):e0191610.

PMID: 29352301 PMC: 5774825. DOI: 10.1371/journal.pone.0191610.

References

Holm L, Rosenstrom P . Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38(Web Server issue):W545-9. PMC: 2896194. DOI: 10.1093/nar/gkq366. View

Liou M, Liu C, Lu C, Hsieh M, Chang K, Kuo H . Genome sequence of Acinetobacter baumannii TYTH-1. J Bacteriol. 2012; 194(24):6974. PMC: 3510636. DOI: 10.1128/JB.01860-12. View

Rossmann M, Moras D, Olsen K . Chemical and biological evolution of nucleotide-binding protein. Nature. 1974; 250(463):194-9. DOI: 10.1038/250194a0. View

Ramirez M, Vilacoba E, Stietz M, Merkier A, Jeric P, Limansky A . Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes. Curr Microbiol. 2013; 67(1):9-14. DOI: 10.1007/s00284-013-0326-5. View

Hoffmann F, Maser E . Carbonyl reductases and pluripotent hydroxysteroid dehydrogenases of the short-chain dehydrogenase/reductase superfamily. Drug Metab Rev. 2007; 39(1):87-144. DOI: 10.1080/03602530600969440. View

Iwashkiw J, Seper A, Weber B, Scott N, Vinogradov E, Stratilo C . Identification of a general O-linked protein glycosylation system in Acinetobacter baumannii and its role in virulence and biofilm formation. PLoS Pathog. 2012; 8(6):e1002758. PMC: 3369928. DOI: 10.1371/journal.ppat.1002758. View

Jornvall H, Hedlund J, Bergman T, Oppermann U, Persson B . Superfamilies SDR and MDR: from early ancestry to present forms. Emergence of three lines, a Zn-metalloenzyme, and distinct variabilities. Biochem Biophys Res Commun. 2010; 396(1):125-30. DOI: 10.1016/j.bbrc.2010.03.094. View

Juhas M, van der Meer J, Gaillard M, Harding R, Hood D, Crook D . Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev. 2009; 33(2):376-93. PMC: 2704930. DOI: 10.1111/j.1574-6976.2008.00136.x. View

Dutta D, Bhattacharyya S, Das A . Crystal structure and fluorescence studies reveal the role of helical dimeric interface of staphylococcal FabG1 in positive cooperativity for NADPH. Proteins. 2012; 80(4):1250-7. DOI: 10.1002/prot.24024. View

10.

Towner K . Acinetobacter: an old friend, but a new enemy. J Hosp Infect. 2009; 73(4):355-63. DOI: 10.1016/j.jhin.2009.03.032. View

11.

Peleg A, Seifert H, Paterson D . Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev. 2008; 21(3):538-82. PMC: 2493088. DOI: 10.1128/CMR.00058-07. View

12.

Kallberg Y, Oppermann U, Jornvall H, Persson B . Short-chain dehydrogenases/reductases (SDRs). Eur J Biochem. 2002; 269(18):4409-17. DOI: 10.1046/j.1432-1033.2002.03130.x. View

13.

Chen V, Arendall 3rd W, Headd J, Keedy D, Immormino R, Kapral G . MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 1):12-21. PMC: 2803126. DOI: 10.1107/S0907444909042073. View

14.

Farrugia D, Elbourne L, Hassan K, Eijkelkamp B, Tetu S, Brown M . The complete genome and phenome of a community-acquired Acinetobacter baumannii. PLoS One. 2013; 8(3):e58628. PMC: 3602452. DOI: 10.1371/journal.pone.0058628. View

15.

Kavanagh K, Jornvall H, Persson B, Oppermann U . Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell Mol Life Sci. 2008; 65(24):3895-906. PMC: 2792337. DOI: 10.1007/s00018-008-8588-y. View

16.

McPhillips T, McPhillips S, Chiu H, Cohen A, Deacon A, Ellis P . Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat. 2002; 9(Pt 6):401-6. DOI: 10.1107/s0909049502015170. View

17.

Philippsen A, Schirmer T, Stein M, Giffhorn F, Stetefeld J . Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution. Acta Crystallogr D Biol Crystallogr. 2005; 61(Pt 4):374-9. DOI: 10.1107/S0907444904034390. View

18.

Oppermann U, Filling C, Hult M, Shafqat N, Wu X, Lindh M . Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chem Biol Interact. 2003; 143-144:247-53. DOI: 10.1016/s0009-2797(02)00164-3. View

19.

Valenzuela J, Thomas L, Partridge S, van der Reijden T, Dijkshoorn L, Iredell J . Horizontal gene transfer in a polyclonal outbreak of carbapenem-resistant Acinetobacter baumannii. J Clin Microbiol. 2006; 45(2):453-60. PMC: 1829019. DOI: 10.1128/JCM.01971-06. View

20.

Eijkelkamp B, Stroeher U, Hassan K, Papadimitrious M, Paulsen I, Brown M . Adherence and motility characteristics of clinical Acinetobacter baumannii isolates. FEMS Microbiol Lett. 2011; 323(1):44-51. DOI: 10.1111/j.1574-6968.2011.02362.x. View