5ZHW

VanYB in complex with D-Alanine-D-Alanine

Summary for 5ZHW

• Entry DOI: 10.2210/pdb5zhw/pdb
• Related: 5ZHF
• Descriptor: D-alanyl-D-alanine carboxypeptidase, COPPER (II) ION, D-ALANINE, ... (6 entities in total)
• Functional Keywords: vancomycin resistance, peptidase, metallopeptidase family m15, hydrolase
• Biological source: Enterococcus faecalis V583
• Total number of polymer chains: 2
• Total formula weight: 52714.18

Authors

Kim, H.S.,Hahn, H. (deposition date: 2018-03-13, release date: 2018-09-05, Last modification date: 2024-10-23)

Primary citation

Kim, H.S.,Hahn, H.,Kim, J.,Jang, D.M.,Lee, J.Y.,Back, J.M.,Im, H.N.,Kim, H.,Han, B.W.,Suh, S.W.
Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.
Int. J. Biol. Macromol., 119:335-344, 2018

PubMed Abstract: Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanY in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala-d-Ala extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanY manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanY in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanY and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanY. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanY around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.

PubMed: 30016658
DOI: 10.1016/j.ijbiomac.2018.07.081

Experimental method

X-RAY DIFFRACTION (2.18 Å)