1b49
From Proteopedia
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|PDB= 1b49 |SIZE=350|CAPTION= <scene name='initialview01'>1b49</scene>, resolution 2.30Å | |PDB= 1b49 |SIZE=350|CAPTION= <scene name='initialview01'>1b49</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=PO4:PHOSPHATE ION'>PO4</scene> | + | |LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b49 OCA], [http://www.ebi.ac.uk/pdbsum/1b49 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b49 RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1B49 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1B49 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B49 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://www.ncbi.nlm.nih.gov/pubmed/10064578 10064578] | 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: Deoxycytidylate 5-hydroxymethyltransferase]] | [[Category: Deoxycytidylate 5-hydroxymethyltransferase]] | ||
| + | [[Category: Enterobacteria phage t4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Sohn, S H.]] | [[Category: Sohn, S H.]] | ||
[[Category: Song, H K.]] | [[Category: Song, H K.]] | ||
[[Category: Suh, S W.]] | [[Category: Suh, S W.]] | ||
| - | [[Category: PO4]] | ||
[[Category: dntp synthesizing complex]] | [[Category: dntp synthesizing complex]] | ||
[[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 30 18:53:15 2008'' |
Revision as of 15:53, 30 March 2008
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| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Deoxycytidylate 5-hydroxymethyltransferase, with EC number 2.1.2.8 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)
Overview
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 Structure
1B49 is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
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:10064578
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