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6gdr

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==DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases==
==DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases==
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<StructureSection load='6gdr' size='340' side='right' caption='[[6gdr]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
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<StructureSection load='6gdr' size='340' side='right'caption='[[6gdr]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6gdr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GDR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6gdr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alteromonas_mediterranea Alteromonas mediterranea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GDR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 2.33&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6gdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gdr OCA], [http://pdbe.org/6gdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gdr RCSB], [http://www.ebi.ac.uk/pdbsum/6gdr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gdr ProSAT]</span></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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6gdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gdr OCA], [https://pdbe.org/6gdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gdr RCSB], [https://www.ebi.ac.uk/pdbsum/6gdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gdr 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/A0A1J0SCU0_9ALTE A0A1J0SCU0_9ALTE]
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DNA ligases join breaks in the phosphodiester backbone of DNA by catalysing the formation of bonds between opposing 5'P and 3'OH ends in an adenylation-dependent manner. Catalysis is accompanied by reorientation of two core domains to provide access to the active site for cofactor utilization and enable substrate binding and product release. The general paradigm is that DNA ligases engage their DNA substrate through complete encirclement of the duplex, completed by inter-domain kissing contacts via loops or additional domains. The recent structure of a minimal Lig E-type DNA ligase, however, implies it must use a different mechanism, as it lacks any domains or loops appending the catalytic core which could complete encirclement. In the present study, we have used a structure-guided mutagenesis approach to investigate the role of conserved regions in the Lig E proteins with respect to DNA binding. We report the structure of a Lig-E type DNA ligase bound to the nicked DNA-adenylate reaction intermediate, confirming that complete encirclement is unnecessary for substrate engagement. Biochemical and biophysical measurements of point mutants to residues implicated in binding highlight the importance of basic residues in the OB domain, and inter-domain contacts to the linker.
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DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.,Williamson A, Grgic M, Leiros HS Nucleic Acids Res. 2018 Jul 11. pii: 5051839. doi: 10.1093/nar/gky622. PMID:30007325<ref>PMID:30007325</ref>
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==See Also==
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*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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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 6gdr" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Grigic, M]]
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[[Category: Alteromonas mediterranea]]
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[[Category: Leiros, H K.S]]
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[[Category: Large Structures]]
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[[Category: Williamson, A]]
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[[Category: Grigic M]]
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[[Category: Dna ligase]]
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[[Category: Leiros HKS]]
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[[Category: Ligase]]
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[[Category: Williamson A]]

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DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases

PDB ID 6gdr

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