4p9c: Difference between revisions
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<StructureSection load='4p9c' size='340' side='right'caption='[[4p9c]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='4p9c' size='340' side='right'caption='[[4p9c]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4p9c]] is a 12 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4p9c]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyanophage_S-TIM5 Cyanophage S-TIM5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P9C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P9C FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</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>, <scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4p9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p9c OCA], [https://pdbe.org/4p9c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p9c RCSB], [https://www.ebi.ac.uk/pdbsum/4p9c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p9c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/H6WFU3_9CAUD H6WFU3_9CAUD] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Cyanophage | [[Category: Cyanophage S-TIM5]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Alian | [[Category: Alian A]] | ||
[[Category: Marx | [[Category: Marx A]] | ||
Latest revision as of 03:41, 28 December 2023
Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dCMP and dUMPCrystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dCMP and dUMP
Structural highlights
FunctionPublication Abstract from PubMedDeoxycytidylate deaminase is unique within the zinc dependent cytidine deaminase family as being allosterically regulated; activated by dCTP and inhibited by dTTP. Here we present the first crystal structure of a dTTP bound deoxycytidylate deaminase from the bacteriophage S-TIM5, confirming that this inhibitor binds to the same site as the dCTP activator. The molecular details of this structure, complemented by structures apo and dCMP bound provide insights into the allosteric mechanism. Whilst the positioning of the nucleoside moiety of dTTP is almost identical to that previously described for dCTP, protonation of N3 in deoxythymidine and not deoxycytidine would facilitate hydrogen bonding of dTTP but not dCTP and may result in a higher affinity of dTTP to the allosteric site conferring its inhibitory activity. Further the functional group on C4 (O in dTTP and NH2 in dCTP) makes interactions with non-conserved protein residues preceding the allosteric motif, and the relative strength of binding to these residues appears to correspond to the potency of dTTP inhibition. The active sites of these structures are also uniquely occupied by dTMP and dCMP resolving aspects of substrate specificity. The methyl group of dTMP apparently clashes with a highly conserved tyrosine residue preventing the formation of a correct base stacking shown to be imperative for deamination activity. The relevance of these finding to the wider zinc dependent cytidine deaminase family is also discussed. The First Crystal Structure of a dTTP Bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site.,Marx A, Alian A J Biol Chem. 2014 Nov 17. pii: jbc.M114.617720. PMID:25404739[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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