1b5d: Difference between revisions
New page: left|200px<br /><applet load="1b5d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1b5d, resolution 2.20Å" /> '''DCMP Hydroxymethylas... |
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[[Image:1b5d.gif|left|200px]]<br /><applet load="1b5d" size=" | [[Image:1b5d.gif|left|200px]]<br /><applet load="1b5d" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1b5d, resolution 2.20Å" /> | caption="1b5d, resolution 2.20Å" /> | ||
'''DCMP Hydroxymethylase from T4 (Intact)'''<br /> | '''DCMP Hydroxymethylase from T4 (Intact)'''<br /> | ||
==Overview== | ==Overview== | ||
Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), a | 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== | ==About this Structure== | ||
1B5D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with DCM as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http:// | 1B5D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=DCM:'>DCM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5D OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Deoxycytidylate 5-hydroxymethyltransferase]] | [[Category: Deoxycytidylate 5-hydroxymethyltransferase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Sohn, S | [[Category: Sohn, S H.]] | ||
[[Category: Song, H | [[Category: Song, H K.]] | ||
[[Category: Suh, S | [[Category: Suh, S W.]] | ||
[[Category: DCM]] | [[Category: DCM]] | ||
[[Category: dntp synthesizing complex]] | [[Category: dntp synthesizing complex]] | ||
[[Category: hydroxymethylase]] | [[Category: hydroxymethylase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:51:39 2008'' | ||
Revision as of 12:51, 21 February 2008
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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 with as ligand. Active as Deoxycytidylate 5-hydroxymethyltransferase, with EC number 2.1.2.8 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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