1b49

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[[Image:1b49.gif|left|200px]]<br /><applet load="1b49" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1b49, resolution 2.30&Aring;" />
 
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'''DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)'''<br />
 
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==Overview==
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==DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)==
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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.
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<StructureSection load='1b49' size='340' side='right'caption='[[1b49]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1b49]] 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=1B49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B49 FirstGlance]. <br>
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1B49 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=PO4:'>PO4</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=1B49 OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b49 OCA], [https://pdbe.org/1b49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b49 RCSB], [https://www.ebi.ac.uk/pdbsum/1b49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b49 ProSAT]</span></td></tr>
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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]
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</table>
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[[Category: Bacteriophage t4]]
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== Function ==
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[[Category: Deoxycytidylate 5-hydroxymethyltransferase]]
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[https://www.uniprot.org/uniprot/DCHM_BPT4 DCHM_BPT4]
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Sohn, S H.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Song, H K.]]
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Check<jmol>
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[[Category: Suh, S W.]]
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<jmolCheckbox>
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[[Category: PO4]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b49_consurf.spt"</scriptWhenChecked>
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[[Category: dntp synthesizing complex]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: hydroxymethylase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:51:16 2008''
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</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=1b49 ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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[[Category: Sohn SH]]
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[[Category: Song HK]]
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[[Category: Suh SW]]

Current revision

DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)

PDB ID 1b49

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