9J4H image
Entry Detail
PDB ID:
9J4H
Keywords:
Title:
Crystal structure of SHMT apo form
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-08-09
Release Date:
2024-10-09
Method Details:
Experimental Method:
Resolution:
2.04 Å
R-Value Free:
0.20
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Serine hydroxymethyltransferase
Chain IDs:A, B, C, D
Chain Length:417
Number of Molecules:4
Biological Source:Enterococcus faecium
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
LLP A LYS modified residue
Ligand Molecules
Primary Citation
SHIN-2 exerts potent activity against VanA-type vancomycin-resistant Enterococcus faecium in vitro by stabilizing the active site loop of serine hydroxymethyltransferase.
Arch.Biochem.Biophys. 761 110160 110160 (2024)
PMID: 39313141 DOI: 10.1016/j.abb.2024.110160

Abstact

Novel classes of antibiotics are needed to improve the resilience of the healthcare system to antimicrobial resistance (AMR), including vancomycin resistance. vanA gene cluster is a cause of vancomycin resistance. This gene cluster is transferred and spreads vancomycin resistance from Enterococcus spp. to Staphylococcus aureus. Therefore, novel antibacterial agents are required to combat AMR, including vanA-type vancomycin resistance. Serine hydroxymethyltransferase (SHMT) is a key target of antibacterial agents. However, the specific binding mechanisms of SHMT inhibitors remain unclear. Detailed structural information will contribute to understanding these mechanisms. In this study, we found that (+)-SHIN-2, the first in vivo active inhibitor of human SHMT, is strongly bound to the Enterococcus faecium SHMT (efmSHMT). Comparison of the crystal structures of apo- and (+)-SHIN-2-boud efmSHMT revealed that (+)-SHIN-2 stabilized the active site loop of efmSHMT via hydrogen bonds, which are critical for efmSHMT inhibition. Additionally, (+)-SHIN-2 formed hydrogen bonds with serine, forming the Schiff's base with pyridoxal 5'-phosphate, which is a co-factor of SHMT. Furthermore, (+)-SHIN-2 exerted biostatic effects on vancomycin-susceptible and vanA-type vancomycin-resistant E. faecium in vitro, indicating that SHMT inhibitors do not induce cross-resistance to vanA-type vancomycin. Overall, these findings can aid in the design of novel SHMT inhibitors to combat AMR, including vancomycin resistance.

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Primary Citation of related structures