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PDBsum entry 1b5d

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1b5d
Jmol
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 hydroxymeth 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08773  (DCHM_BPT4) -  Deoxycytidylate 5-hydroxymethyltransferase
Seq:
Struc:
246 a.a.
246 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.2.8  - Deoxycytidylate 5-hydroxymethyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 5,10-methylenetetrahydrofolate + H2O + deoxycytidylate = tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
5,10-methylenetetrahydrofolate
+ H(2)O
+
deoxycytidylate
Bound ligand (Het Group name = DCM)
corresponds exactly
= tetrahydrofolate
+ 5-hydroxymethyldeoxycytidylate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methylation   2 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    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.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
20627870 T.Xu, F.Yao, X.Zhou, Z.Deng, and D.You (2010).
A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.
  Nucleic Acids Res, 38, 7133-7141.  
  19411852 L.M.Iyer, M.Tahiliani, A.Rao, and L.Aravind (2009).
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.
  Cell Cycle, 8, 1698-1710.  
18065532 P.J.Ceyssens, V.Mesyanzhinov, N.Sykilinda, Y.Briers, B.Roucourt, R.Lavigne, J.Robben, A.Domashin, K.Miroshnikov, G.Volckaert, and K.Hertveldt (2008).
The genome and structural proteome of YuA, a new Pseudomonas aeruginosa phage resembling M6.
  J Bacteriol, 190, 1429-1435.  
12626685 E.S.Miller, E.Kutter, G.Mosig, F.Arisaka, T.Kunisawa, and W.Rüger (2003).
Bacteriophage T4 genome.
  Microbiol Mol Biol Rev, 67, 86.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.