1b5d: Difference between revisions
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|PDB= 1b5d |SIZE=350|CAPTION= <scene name='initialview01'>1b5d</scene>, resolution 2.20Å | |PDB= 1b5d |SIZE=350|CAPTION= <scene name='initialview01'>1b5d</scene>, resolution 2.20Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=DCM:2 | |LIGAND= <scene name='pdbligand=DCM:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DCM</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Deoxycytidylate_5-hydroxymethyltransferase Deoxycytidylate 5-hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.8 2.1.2.8] | |ACTIVITY= [http://en.wikipedia.org/wiki/Deoxycytidylate_5-hydroxymethyltransferase Deoxycytidylate 5-hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.8 2.1.2.8] | ||
|GENE= | |GENE= | ||
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[[Category: hydroxymethylase]] | [[Category: hydroxymethylase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 11:12:38 2008'' | ||
Revision as of 12:12, 23 March 2008
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| , resolution 2.20Å | |||||||
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| Ligands: | |||||||
| Activity: | Deoxycytidylate 5-hydroxymethyltransferase, with EC number 2.1.2.8 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DCMP Hydroxymethylase from T4 (Intact)
OverviewOverview
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.
About this StructureAbout this Structure
1B5D is a Single protein structure of sequence from Bacteriophage t4. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex., Song HK, Sohn SH, Suh SW, EMBO J. 1999 Mar 1;18(5):1104-13. PMID:10064578
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