3ta5

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Current revision (13:22, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3ta5' size='340' side='right'caption='[[3ta5]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
<StructureSection load='3ta5' size='340' side='right'caption='[[3ta5]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ta5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"candidatus_korarchaeum_cryptofilum"_elkins_et_al._2008 "candidatus korarchaeum cryptofilum" elkins et al. 2008]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TA5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TA5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ta5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Korarchaeum_cryptofilum Candidatus Korarchaeum cryptofilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TA5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TA5 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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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]] 1.52&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3p4h|3p4h]], [[3ta7|3ta7]]</div></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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Kcr_0736 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=498846 "Candidatus Korarchaeum cryptofilum" Elkins et al. 2008])</td></tr>
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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=3ta5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ta5 OCA], [https://pdbe.org/3ta5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ta5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ta5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ta5 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ta5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ta5 OCA], [https://pdbe.org/3ta5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ta5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ta5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ta5 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/B1L4V6_KORCO B1L4V6_KORCO]
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LigD 3'-phosphoesterase (PE) enzymes perform end-healing reactions at DNA breaks. Here we characterize the 3'-ribonucleoside-resecting activity of Candidatus Korarchaeum PE. CkoPE prefers a single-stranded substrate versus a primer-template. Activity is abolished by vanadate (10 mM), but is less sensitive to phosphate (IC(50) 50 mM) or chloride (IC(50) 150 mM). The metal requirement is satisfied by manganese, cobalt, copper or cadmium, but not magnesium, calcium, nickel or zinc. Insights to CkoPE metal specificity were gained by solving new 1.5 A crystal structures of CkoPE in complexes with Co(2+) and Zn(2+). His9, His15 and Asp17 coordinate cobalt in an octahedral complex that includes a phosphate anion, which is in turn coordinated by Arg19 and His51. The cobalt and phosphate positions and the atomic contacts in the active site are virtually identical to those in the CkoPE.Mn(2+) structure. By contrast, Zn(2+) binds in the active site in a tetrahedral complex, wherein the position, orientation and atomic contacts of the phosphate are shifted and its interaction with His51 is lost. We conclude that: (i) PE selectively binds to 'soft' metals in either productive or non-productive modes and (ii) PE catalysis depends acutely on proper metal and scissile phosphate geometry.
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Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.,Das U, Smith P, Shuman S Nucleic Acids Res. 2012 Jan 1;40(2):828-36. Epub 2011 Sep 28. PMID:21965539<ref>PMID:21965539</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ta5" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Candidatus korarchaeum cryptofilum elkins et al. 2008]]
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[[Category: Candidatus Korarchaeum cryptofilum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Das, U]]
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[[Category: Das U]]
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[[Category: Shuman, S]]
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[[Category: Shuman S]]
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[[Category: Smith, P]]
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[[Category: Smith P]]
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[[Category: 3'-phosphoesterase]]
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[[Category: Hydrolase]]
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Current revision

Cobalt bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family

PDB ID 3ta5

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