Structural Characterization of MepB from Staphylococcus Aureus Reveals Homology to Endonucleases

Overview

Journal Protein Sci

Specialty Biochemistry

Date 2014 Feb 7

PMID 24501097

Citations 4

Authors

Sayeh Agah

Sandra Poulos

Christian Banchs

Salem Faham

Affiliations

Soon will be listed here.

Abstract

The MepRAB operon in Staphylococcus aureus has been identified to play a role in drug resistance. Although the functions of MepA and MepR are known, little information is available on the function of MepB. Here we report the X-ray structure of MepB to 2.1 Å revealing its structural similarity to the PD-(D/E)XK family of endonucleases. We further show that MepB binds DNA and RNA, with a higher affinity towards RNA and single stranded DNA than towards double stranded DNA. Notably, the PD-(D/E)XK catalytic active site residues are not conserved in MepB. MepB's association with a drug resistance operon suggests that it plays a role in responding to antimicrobials. This role is likely carried out through MepB's interactions with nucleic acids.

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References

. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 5):760-3. DOI: 10.1107/S0907444994003112. View

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

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

Krissinel E, Henrick K . Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007; 372(3):774-97. DOI: 10.1016/j.jmb.2007.05.022. View

Huet A, Raygada J, Mendiratta K, Seo S, Kaatz G . Multidrug efflux pump overexpression in Staphylococcus aureus after single and multiple in vitro exposures to biocides and dyes. Microbiology (Reading). 2008; 154(Pt 10):3144-3153. DOI: 10.1099/mic.0.2008/021188-0. View

Emsley P, Cowtan K . Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004; 60(Pt 12 Pt 1):2126-32. DOI: 10.1107/S0907444904019158. View

Alekshun M, Levy S . Molecular mechanisms of antibacterial multidrug resistance. Cell. 2007; 128(6):1037-50. DOI: 10.1016/j.cell.2007.03.004. View

Kaatz G, Moudgal V, Seo S . Identification and characterization of a novel efflux-related multidrug resistance phenotype in Staphylococcus aureus. J Antimicrob Chemother. 2002; 50(6):833-8. DOI: 10.1093/jac/dkf224. View

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

10.

Kaatz G, McAleese F, Seo S . Multidrug resistance in Staphylococcus aureus due to overexpression of a novel multidrug and toxin extrusion (MATE) transport protein. Antimicrob Agents Chemother. 2005; 49(5):1857-64. PMC: 1087643. DOI: 10.1128/AAC.49.5.1857-1864.2005. View

11.

Kaatz G, DeMarco C, Seo S . MepR, a repressor of the Staphylococcus aureus MATE family multidrug efflux pump MepA, is a substrate-responsive regulatory protein. Antimicrob Agents Chemother. 2006; 50(4):1276-81. PMC: 1426934. DOI: 10.1128/AAC.50.4.1276-1281.2006. View

12.

Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K . Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res. 2012; 40(15):7016-45. PMC: 3424549. DOI: 10.1093/nar/gks382. View

13.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

14.

Singer V, Lawlor T, Yue S . Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test). Mutat Res. 1999; 439(1):37-47. DOI: 10.1016/s1383-5718(98)00172-7. View

15.

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

16.

Murshudov G, Vagin A, Dodson E . Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997; 53(Pt 3):240-55. DOI: 10.1107/S0907444996012255. View

17.

Cheng X, Balendiran K, Schildkraut I, Anderson J . Structure of PvuII endonuclease with cognate DNA. EMBO J. 1994; 13(17):3927-35. PMC: 395312. DOI: 10.1002/j.1460-2075.1994.tb06708.x. View

18.

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

19.

Lovell S, Davis I, Arendall 3rd W, de Bakker P, Word J, Prisant M . Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003; 50(3):437-50. DOI: 10.1002/prot.10286. View

20.

Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T . ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 2005; 33(Web Server issue):W299-302. PMC: 1160131. DOI: 10.1093/nar/gki370. View