PDBsum entry 2vmp

Transferase

PDB id: 2vmp

Contents

Protein chain

405 a.a. *

Ligands

SER-PLP

MPD ×2

PO4

Waters ×400

* Residue conservation analysis

PDB id:

2vmp

Name:

Transferase

Title:

Crystal structure of n341absshmt l-ser external aldimine

Structure:

Serine hydroxymethyltransferase. Chain: a. Fragment: residues 1-405. Synonym: shmt, serine methylase. Engineered: yes. Mutation: yes. Other_details: schiff linkage between l-ser b 502 and plp b 501

Source:

Bacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.74Å R-factor: 0.184 R-free: 0.217

Authors:

V.Rajaram,V.R.Pai,S.Bisht,B.S.Bhavani,N.Appaji Rao,H.S.Savithri, M.R.N.Murthy

Key ref:

V.R.Pai et al. (2009). Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding. Biochem J, 418, 635-642. PubMed id: 19046138

Date:

29-Jan-08 Release date: 16-Dec-08

Protein chain

Q7SIB6  (Q7SIB6_GEOSE) -  Serine hydroxymethyltransferase from Geobacillus stearothermophilus

Seq: 419 a.a.

Struc: 405 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 = SER) corresponds exactly)

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

Biochem J 418:635-642 (2009)

PubMed id: 19046138

Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding.

V.R.Pai, V.Rajaram, S.Bisht, B.S.Bhavani, N.A.Rao, M.R.Murthy, H.S.Savithri.

ABSTRACT

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THF. SHMT also catalyses several THF-independent side reactions such as cleavage of beta-hydroxy amino acids, transamination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect on either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.