1b5d: Difference between revisions

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[[Image:1b5d.gif|left|200px]]


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==DCMP Hydroxymethylase from T4 (Intact)==
The line below this paragraph, containing "STRUCTURE_1b5d", creates the "Structure Box" on the page.
<StructureSection load='1b5d' size='340' side='right'caption='[[1b5d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1b5d]] 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=1B5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B5D FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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>
{{STRUCTURE_1b5d|  PDB=1b5d  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b5d OCA], [https://pdbe.org/1b5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b5d RCSB], [https://www.ebi.ac.uk/pdbsum/1b5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b5d ProSAT]</span></td></tr>
 
</table>
'''DCMP Hydroxymethylase from T4 (Intact)'''
== Function ==
 
[https://www.uniprot.org/uniprot/DCHM_BPT4 DCHM_BPT4]  
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b5/1b5d_consurf.spt"</scriptWhenChecked>
1B5D 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=1B5D OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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]
</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=1b5d ConSurf].
[[Category: Deoxycytidylate 5-hydroxymethyltransferase]]
<div style="clear:both"></div>
[[Category: Enterobacteria phage t4]]
__TOC__
[[Category: Single protein]]
</StructureSection>
[[Category: Sohn, S H.]]
[[Category: Escherichia virus T4]]
[[Category: Song, H K.]]
[[Category: Large Structures]]
[[Category: Suh, S W.]]
[[Category: Sohn SH]]
[[Category: Dntp synthesizing complex]]
[[Category: Song HK]]
[[Category: Hydroxymethylase]]
[[Category: Suh SW]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 11:05:33 2008''

Latest revision as of 06:34, 7 February 2024

DCMP Hydroxymethylase from T4 (Intact)

1b5d, resolution 2.20Å

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