PDBsum entry 1b5d

Transferase

PDB id: 1b5d

Contents

Protein chains

246 a.a. *

Ligands

DCM ×2

Waters ×151

* Residue conservation analysis

PDB id:

1b5d

Name:

Transferase

Title:

Dcmp hydroxymethylase from t4 (intact)

Structure:

Protein (deoxycytidylate hydroxymethylase). Chain: a, b. Synonym: deoxycytidylate hydroxymethylase, dcmp hydroxymethylase. Ec: 2.1.2.8

Source:

Enterobacteria phage t4. Organism_taxid: 10665

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.160 R-free: 0.208

Authors:

H.K.Song,S.H.Sohn,S.W.Suh

Key ref:

H.K.Song et al. (1999). Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex. EMBO J, 18, 1104-1113. PubMed id: 10064578 DOI: 10.1093/emboj/18.5.1104

Date:

06-Jan-99 Release date: 13-Jan-99

Protein chains

P08773  (DCHM_BPT4) -  Deoxycytidylate 5-hydroxymethyltransferase from Enterobacteria phage T4

Seq: 246 a.a.

Struc: 246 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.2.8 - deoxycytidylate 5-hydroxymethyltransferase.
• Reaction: dCMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H2O = 5-hydroxymethyl-dCMP + (6S)-5,6,7,8-tetrahydrofolate

dCMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate (Bound ligand (Het Group name = DCM) corresponds exactly) + H2O = 5-hydroxymethyl-dCMP + (6S)-5,6,7,8-tetrahydrofolate

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

Key reference

DOI no: 10.1093/emboj/18.5.1104

EMBO J 18:1104-1113 (1999)

PubMed id: 10064578

Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.

H.K.Song, S.H.Sohn, S.W.Suh.

ABSTRACT

Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), a homodimer of 246-residue subunits, catalyzes hydroxymethylation of the cytosine base in deoxycytidylate (dCMP) to produce 5-hydroxymethyl-dCMP. It forms part of a phage DNA protection system and appears to function in vivo as a component of a multienzyme complex called deoxyribonucleoside triphosphate (dNTP) synthetase. We have determined its crystal structure in the presence of the substrate dCMP at 1.6 A resolution. The structure reveals a subunit fold and a dimerization pattern in common with thymidylate synthases, despite low (approximately 20%) sequence identity. Among the residues that form the dCMP binding site, those interacting with the sugar and phosphate are arranged in a configuration similar to the deoxyuridylate binding site of thymidylate synthases. However, the residues interacting directly or indirectly with the cytosine base show a more divergent structure and the presumed folate cofactor binding site is more open. Our structure reveals a water molecule properly positioned near C-6 of cytosine to add to the C-7 methylene intermediate during the last step of hydroxymethylation. On the basis of sequence comparison and crystal packing analysis, a hypothetical model for the interaction between T4 deoxycytidylate hydroxymethylase and T4 thymidylate synthase in the dNTP-synthesizing complex has been built.

Selected figure(s)

Figure 4.
Figure 4 Ribbon diagram comparing the subunit folds of T4 CH (left) and E.coli TS (right). The structurally similar parts are colored in blue and the remaining parts in orange. The catalytically important residues (Glu60, Cys148 and Asp179 in T4 CH; Glu58, Cys146 and Asn177 in E.coli TS) are shown in green. The substrates dCMP in T4 CH and dUMP in E.coli TS are drawn in deep blue and the cofactor analog CB3717 bound to E.coli TS is in magenta. This figure was drawn by MOLSCRIPT (Kraulis, 1991) and RASTER 3D (Merritt and Murphy, 1994).

Figure 5.
Figure 5 Schematic diagram of the hydrogen-bond network in the active site of T4 CH. The distance between the S atom of Cys148 and the guanidium group of Arg168 (3.3 Å) is indicated.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 1104-1113) copyright 1999.

Figures were selected by an automated process.