5c2f
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5c2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C2F FirstGlance]. <br> | <table><tr><td colspan='2'>[[5c2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C2F FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JTH:2,7-DIHYDROXY-4-(PROPAN-2-YL)CYCLOHEPTA-2,4,6-TRIEN-1-ONE'>JTH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.86Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JTH:2,7-DIHYDROXY-4-(PROPAN-2-YL)CYCLOHEPTA-2,4,6-TRIEN-1-ONE'>JTH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c2f OCA], [https://pdbe.org/5c2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c2f RCSB], [https://www.ebi.ac.uk/pdbsum/5c2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c2f 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=5c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c2f OCA], [https://pdbe.org/5c2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c2f RCSB], [https://www.ebi.ac.uk/pdbsum/5c2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c2f ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/Q716H3_BPSFV Q716H3_BPSFV] | [https://www.uniprot.org/uniprot/Q716H3_BPSFV Q716H3_BPSFV] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg2+ from Ca2+. Using a metal ion chelator beta-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution. | ||
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| - | Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism.,Zhao H, Lin Z, Lynn AY, Varnado B, Beutler JA, Murelli RP, Le Grice SF, Tang L Nucleic Acids Res. 2015 Oct 7. pii: gkv1018. PMID:26450964<ref>PMID:26450964</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 5c2f" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Terminase 3D Structures|Terminase 3D Structures]] | *[[Terminase 3D Structures|Terminase 3D Structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
K428A mutant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese and beta-thujaplicinol
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