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6ras

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Current revision (07:37, 1 May 2024) (edit) (undo)
 
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<StructureSection load='6ras' size='340' side='right'caption='[[6ras]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
<StructureSection load='6ras' size='340' side='right'caption='[[6ras]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ras]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Prochlorococcus_marinus_str._mit_9302 Prochlorococcus marinus str. mit 9302]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAS FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ras]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/DNA_launch_vector_pDE-GFP2 DNA launch vector pDE-GFP2] and [https://en.wikipedia.org/wiki/Prochlorococcus_marinus_str._MIT_9302 Prochlorococcus marinus str. MIT 9302]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RAS 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=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.75&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></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=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EU96_0746 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=74545 Prochlorococcus marinus str. MIT 9302])</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=6ras FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ras OCA], [https://pdbe.org/6ras PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ras RCSB], [https://www.ebi.ac.uk/pdbsum/6ras PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ras ProSAT]</span></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=6ras FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ras OCA], [http://pdbe.org/6ras PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ras RCSB], [http://www.ebi.ac.uk/pdbsum/6ras PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ras ProSAT]</span></td></tr>
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</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/A0A0A2ACP7_PROMR A0A0A2ACP7_PROMR]
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DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.
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Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.,Williamson A, Leiros HS Nucleic Acids Res. 2019 Aug 22;47(14):7147-7162. doi: 10.1093/nar/gkz596. PMID:31312841<ref>PMID:31312841</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 6ras" 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: DNA launch vector pDE-GFP2]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Prochlorococcus marinus str. mit 9302]]
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[[Category: Prochlorococcus marinus str. MIT 9302]]
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[[Category: Leiros, H K.S]]
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[[Category: Leiros HKS]]
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[[Category: Williamson, A]]
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[[Category: Williamson A]]
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[[Category: Atp-dependent]]
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[[Category: Determinants in dna binding]]
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[[Category: Dna binding protein]]
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[[Category: Dna ligase]]
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[[Category: Ligase-dna co-crystal structure]]
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Current revision

Pmar-Lig_Pre.

PDB ID 6ras

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