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| [[Image:1b5e.gif|left|200px]]<br /><applet load="1b5e" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1b5e, resolution 1.60Å" />
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| '''DCMP HYDROXYMETHYLASE FROM T4'''<br />
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| ==Overview== | | ==DCMP HYDROXYMETHYLASE FROM T4== |
| 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.
| | <StructureSection load='1b5e' size='340' side='right'caption='[[1b5e]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1b5e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B5E FirstGlance]. <br> |
| 1B5E is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t2 Enterobacteria phage t2] 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] Known structural/functional Site: <scene name='pdbsite=CAT:The+Sg+Atom+Of+CYS+148+Has+Dual+conform.'>CAT</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5E OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene></td></tr> |
| ==Reference==
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b5e OCA], [https://pdbe.org/1b5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b5e RCSB], [https://www.ebi.ac.uk/pdbsum/1b5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b5e ProSAT]</span></td></tr> |
| 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10064578 10064578]
| | </table> |
| [[Category: Deoxycytidylate 5-hydroxymethyltransferase]] | | == Function == |
| [[Category: Enterobacteria phage t2]] | | [https://www.uniprot.org/uniprot/DCHM_BPT4 DCHM_BPT4] |
| [[Category: Single protein]] | | == Evolutionary Conservation == |
| [[Category: Sohn, S H.]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| [[Category: Song, H K.]] | | Check<jmol> |
| [[Category: Suh, S W.]] | | <jmolCheckbox> |
| [[Category: DCM]] | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b5/1b5e_consurf.spt"</scriptWhenChecked> |
| [[Category: dntp synthesizing complex]] | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| [[Category: hydroxymethylase]] | | <text>to colour the structure by Evolutionary Conservation</text> |
| | | </jmolCheckbox> |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:51:46 2008''
| | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1b5e ConSurf]. |
| | <div style="clear:both"></div> |
| | __TOC__ |
| | </StructureSection> |
| | [[Category: Escherichia virus T4]] |
| | [[Category: Large Structures]] |
| | [[Category: Sohn SH]] |
| | [[Category: Song HK]] |
| | [[Category: Suh SW]] |
