4ECL

Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg

Summary for 4ECL

• Entry DOI: 10.2210/pdb4ecl/pdb
• Descriptor: Serine racemase, CHLORIDE ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: antibiotic resistance, vancomycin resistance, center for structural genomics of infectious diseases (csgid), alpha/beta barrel, tim barrel, type iii pyridoxal 5-phosphate (plp)-dependent enzyme, acyltransferase family, l-serine racemase, d-serine racemase, isomerase, l-serine, d-serine, plp, pyridoxal 5-phosphate, cytoplasmic
• Biological source: Enterococcus faecalis
• Total number of polymer chains: 4
• Total formula weight: 167411.39

Authors

Stogios, P.J.,Wawrzak, Z.,Minasov, G.,Evdokimova, E.,Egorova, O.,Cosme, J.,Di Leo, R.,Krishnamoorthy, M.,Meziane-Cherif, D.,Courvalin, P.,Savchenko, A.,Anderson, W.F.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2012-03-26, release date: 2012-04-18, Last modification date: 2024-11-06)

Primary citation

Meziane-Cherif, D.,Stogios, P.J.,Evdokimova, E.,Egorova, O.,Savchenko, A.,Courvalin, P.
Structural and Functional Adaptation of Vancomycin Resistance VanT Serine Racemases.
MBio, 6:e00806-e00806, 2015

PubMed Abstract: Vancomycin resistance in Gram-positive bacteria results from the replacement of the D-alanyl-D-alanine target of peptidoglycan precursors with D-alanyl-D-lactate or D-alanyl-D-serine (D-Ala-D-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of D-Ala-D-Ser-terminating precursors by converting L-Ser to D-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in L-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5'-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for the L-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against L-Ser versus L-Ala implied that this enzyme relies on its membrane-bound domain for L-Ser transport to increase the overall rate of d-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria.

PubMed: 26265719
DOI: 10.1128/mBio.00806-15

Experimental method

X-RAY DIFFRACTION (2.017 Å)