PDBsum entry 2w7f

Transferase

PDB id: 2w7f

Contents

Protein chain

405 a.a. *

Ligands

SER-PLP

MPD ×2

PO4

Waters ×435

* Residue conservation analysis

PDB id:

2w7f

Name:

Transferase

Title:

Crystal structure of y51fbsshmt l-ser external aldimine

Structure:

Serine hydroxymethyltransferase. Chain: a. Fragment: residues 1-405. Engineered: yes. Mutation: yes. Other_details: schiff linkage between lys a226 and plp a501

Source:

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

Resolution:

1.67Å R-factor: 0.182 R-free: 0.211

Authors:

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

Key ref:

B.S.Bhavani et al. (2008). Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and L-allo-Thr cleavage. Febs J, 275, 4606-4619. PubMed id: 18699779

Date:

22-Dec-08 Release date: 18-Aug-10

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

Febs J 275:4606-4619 (2008)

PubMed id: 18699779

Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and L-allo-Thr cleavage.

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

ABSTRACT

Serine hydroxymethyltransferase (SHMT) from Bacillus stearothermophilus (bsSHMT) is a pyridoxal 5'-phosphate-dependent enzyme that catalyses the conversion of L-serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. In addition, the enzyme catalyses the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids and transamination. In this article, we have examined the mechanism of the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids by SHMT. The three-dimensional structure and biochemical properties of Y51F and Y61A bsSHMTs and their complexes with substrates, especially L-allo-Thr, show that the cleavage of 3-hydroxy amino acids could proceed via Calpha proton abstraction rather than hydroxyl proton removal. Both mutations result in a complete loss of tetrahydrofolate-dependent and tetrahydrofolate-independent activities. The mutation of Y51 to F strongly affects the binding of pyridoxal 5'-phosphate, possibly as a consequence of a change in the orientation of the phenyl ring in Y51F bsSHMT. The mutant enzyme could be completely reconstituted with pyridoxal 5'-phosphate. However, there was an alteration in the lambda max value of the internal aldimine (396 nm), a decrease in the rate of reduction with NaCNBH3 and a loss of the intermediate in the interaction with methoxyamine (MA). The mutation of Y61 to A results in the loss of interaction with Calpha and Cbeta of the substrates. X-Ray structure and visible CD studies show that the mutant is capable of forming an external aldimine. However, the formation of the quinonoid intermediate is hindered. It is suggested that Y61 is involved in the abstraction of the Calpha proton from 3-hydroxy amino acids. A new mechanism for the cleavage of 3-hydroxy amino acids via Calpha proton abstraction by SHMT is proposed.