1b5d: Difference between revisions
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'''DCMP Hydroxymethylase from T4 (Intact)''' | {{Structure | ||
|PDB= 1b5d |SIZE=350|CAPTION= <scene name='initialview01'>1b5d</scene>, resolution 2.20Å | |||
|SITE= | |||
|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] | |||
|GENE= | |||
}} | |||
'''DCMP Hydroxymethylase from T4 (Intact)''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1B5D is a [ | 1B5D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5D OCA]. | ||
==Reference== | ==Reference== | ||
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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10064578 10064578] | ||
[[Category: Bacteriophage t4]] | [[Category: Bacteriophage t4]] | ||
[[Category: Deoxycytidylate 5-hydroxymethyltransferase]] | [[Category: Deoxycytidylate 5-hydroxymethyltransferase]] | ||
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[[Category: hydroxymethylase]] | [[Category: hydroxymethylase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:06:27 2008'' | ||
Revision as of 11:06, 20 March 2008
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| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| 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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