PDBsum entry 4p3m

Transferase

PDB id: 4p3m

Contents

Protein chains

376 a.a.

Ligands

SO4 ×5

GOL ×7

Metals

_CL ×3

Waters ×548

PDB id:

4p3m

Name:

Transferase

Title:

Crystal structure of serine hydroxymethyltransferase from psychromonas ingrahamii

Structure:

Serine hydroxymethyltransferase. Chain: a, b. Synonym: serine methylase. Engineered: yes

Source:

Psychromonas ingrahamii. Organism_taxid: 357804. Strain: 37. Gene: glya, ping_1438. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.85Å R-factor: 0.170 R-free: 0.212

Authors:

F.Dworkowski,S.Angelaccio,S.Pascarella,G.Capitani

Key ref:

S.Angelaccio et al. (2014). Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii. Proteins, 82, 2831-2841. PubMed id: 25044250 DOI: 10.1002/prot.24646

Date:

09-Mar-14 Release date: 30-Jul-14

Protein chains

A1SUU0  (GLYA_PSYIN) -  Serine hydroxymethyltransferase from Psychromonas ingrahamii (strain DSM 17664 / CCUG 51855 / 37)

Seq: 421 a.a.

Struc: 376 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.2.1 - glycine hydroxymethyltransferase.
• Pathway: Folate Coenzymes
• Reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)- 5,6,7,8-tetrahydrofolate + L-serine

(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)- 5,6,7,8-tetrahydrofolate + L-serine (Bound ligand (Het Group name = GOL) matches with 62.50% similarity)

• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/prot.24646

Proteins 82:2831-2841 (2014)

PubMed id: 25044250

Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii.

S.Angelaccio, F.Dworkowski, A.Di Bello, T.Milano, G.Capitani, S.Pascarella.

ABSTRACT

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the reversible conversion of l-serine and tetrahydropteroylglutamate (H4 PteGlu) to glycine and 5,10-methylenetetrahydropteroylglutamate (5,10-CH2 -H4 PteGlu). The SHMT from the psychrophilic bacterium Psychromonas ingrahamii (piSHMT) had been recently purified and characterized. This enzyme was shown to display catalytic and stability properties typical of psychrophilic enzymes, namely high catalytic activity at low temperature and thermolability. To gain deeper insights into the structure-function relationship of piSHMT, the three-dimensional structure of its apo form was determined by X-ray crystallography. Homology modeling techniques were applied to build a model of the piSHMT holo form. Comparison of the two forms unraveled the conformation modifications that take place when the apo enzyme binds its cofactor. Our results show that the apo form is in an "open" conformation and possesses four (or five, in chain A) disordered loops whose electron density is not visible by X-ray crystallography. These loops contain residues that interact with the PLP cofactor and three of them are localized in the major domain that, along with the small domain, constitutes the single subunit of the SHMT homodimer. Cofactor binding triggers a rearrangement of the small domain that moves toward the large domain and screens the PLP binding site at the solvent side. Comparison to the mesophilic apo SHMT from Salmonella typhimurium suggests that the backbone conformational changes are wider in psychrophilic SHMT. Proteins 2014; 82:2831-2841. © 2014 Wiley Periodicals, Inc.