PDBsum entry: 1kl1

Transferase

PDB id: 1kl1

Contents

Protein chain

405 a.a. *

Ligands

PLP-GLY

Waters ×245

* Residue conservation analysis

PDB id:

1kl1

Name:

Transferase

Title:

Crystal structure of serine hydroxymethyltransferase complex glycine

Structure:

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

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.93Å R-factor: 0.170 R-free: 0.197

Authors:

V.Trivedi,A.Gupta,V.R.Jala,P.Saravanan,G.S.J.Rao,N.A.Rao, H.S.Savithri,H.S.Subramanya

Key ref:

V.Trivedi et al. (2002). Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism. J Biol Chem, 277, 17161-17169. PubMed id: 11877399 DOI: 10.1074/jbc.M111976200

Date:

11-Dec-01 Release date: 10-Jul-02

Protein chain

Q7SIB6  (Q7SIB6_GEOSE) -  Serine hydroxymethyltransferase

Seq: 419 a.a.

Struc: 405 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.2.1 - Glycine hydroxymethyltransferase.
• Pathway: Folate Coenzymes
• Reaction: 5,10-methylenetetrahydrofolate + glycine + H₂O = tetrahydrofolate + L-serine

5,10-methylenetetrahydrofolate + glycine (Bound ligand (Het Group name = GLY) corresponds exactly) + H(2)O = tetrahydrofolate + L-serine

• 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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: one-carbon metabolic process (4 terms)
• Biochemical function: catalytic activity (4 terms)

reference

DOI no: 10.1074/jbc.M111976200

J Biol Chem 277:17161-17169 (2002)

PubMed id: 11877399

Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism.

V.Trivedi, A.Gupta, V.R.Jala, P.Saravanan, G.S.Rao, N.A.Rao, H.S.Savithri, H.S.Subramanya.

ABSTRACT

Serine hydroxymethyltransferase (SHMT), a member of the alpha-class of pyridoxal phosphate-dependent enzymes, catalyzes the reversible conversion of serine to glycine and tetrahydrofolate to 5,10-methylene tetrahydrofolate. We present here the crystal structures of the native enzyme and its complexes with serine, glycine, glycine, and 5-formyl tetrahydrofolate (FTHF) from Bacillus stearothermophilus. The first structure of the serine-bound form of SHMT allows identification of residues involved in serine binding and catalysis. The SHMT-serine complex does not show any significant conformational change compared with the native enzyme, contrary to that expected for a conversion from an "open" to "closed" form of the enzyme. However, the ternary complex with FTHF and glycine shows the reported conformational changes. In contrast to the Escherichia coli enzyme, this complex shows asymmetric binding of the FTHF to the two monomers within the dimer in a way similar to the murine SHMT. Comparison of the ternary complex with the native enzyme reveals the structural basis for the conformational change and asymmetric binding of FTHF. The four structures presented here correspond to the various reaction intermediates of the catalytic pathway and provide evidence for a direct displacement mechanism for the hydroxymethyl transfer rather than a retroaldol cleavage.

Selected figure(s)

Figure 1.
Fig. 1. The overall fold of the dimer of native bsSHMT , prepared using the program MOLSCRIPT (41). The cofactor PLP is shown in the ball and stick representation.

Figure 4.
Fig. 4. Stereoview of the overlaid structures of the monomer A (showing good density for the FTHF ) of bsSHMT ternary complex (red) and the native structure (green) showing differences in the conformations of the C-terminal domain and parts of the N-terminal domain. The program MOLSCRIPT (41) was used to prepare this figure.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 17161-17169) copyright 2002.

Figures were selected by the author.