9kro

From Proteopedia

Crystal structure of SHMT from E. faecium with mangiferin

Structural highlights

9kro is a 2 chain structure with sequence from Enterococcus faecium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A133CK16_ENTFC Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051]

Publication Abstract from PubMed

Serine hydroxymethyltransferase (SHMT) plays a critical role in the 1C metabolism pathway. This pathway is involved in the synthesis of many amino and nucleic acids, and SHMT is considered a target for drugs through folate metabolism, especially for cancer and malaria. A detailed analysis of the interactions between SHMTs and drugs will greatly contribute to the development of new drugs. An anthraquinone compound was found in a compound library screening against SHMT from Enterococcus faecium (efmSHMT), from which mangiferin was implied as a compound that binds to efmSHMT. The binding assay indicated that mangiferin could bind to efmSHMT, and crystal structure analysis revealed interactions between efmSHMT and mangiferin at the binding site. Mangiferin bound to the binding site, turning the glucose moiety inward, which was supported by the docking model study. Although mangiferin does not share its molecular structure with other known inhibitors, such as pyrazolopyran-based compounds, the complex structure of the binding site did not differ much from those of other structures. The ligand binding site of efmSHMT may possess a preferred conformation.

Binding of a potential antibacterial drug, mangiferin, to serine hydroxymethyltransferase from Enterococcus faecium.,Hayashi H, Hasegawa K, Saijo E, Kodama EN, Murayama K Biochem Biophys Res Commun. 2025 Jan;743:151177. doi: 10.1016/j.bbrc.2024.151177. , Epub 2024 Dec 12. PMID:39693942^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hayashi H, Hasegawa K, Saijo E, Kodama EN, Murayama K. Binding of a potential antibacterial drug, mangiferin, to serine hydroxymethyltransferase from Enterococcus faecium. Biochem Biophys Res Commun. 2025 Jan;743:151177. PMID:39693942 doi:10.1016/j.bbrc.2024.151177