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1B49

DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)

Summary for 1B49
Entry DOI10.2210/pdb1b49/pdb
DescriptorPROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE), PHOSPHATE ION (3 entities in total)
Functional Keywordshydroxymethylase, dntp synthesizing complex, transferase
Biological sourceEnterobacteria phage T4
Total number of polymer chains2
Total formula weight57236.40
Authors
Song, H.K.,Sohn, S.H.,Suh, S.W. (deposition date: 1999-01-06, release date: 1999-01-13, Last modification date: 2024-02-07)
Primary citationSong, H.K.,Sohn, S.H.,Suh, S.W.
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
EMBO J., 18:1104-1113, 1999
Cited by
PubMed 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.
PubMed: 10064578
DOI: 10.1093/emboj/18.5.1104
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.3 Å)
Structure validation

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