5c2d

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==K428A mutant gp2c of large terminase subunit from bacteriophage sf6 with calcium==
==K428A mutant gp2c of large terminase subunit from bacteriophage sf6 with calcium==
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<StructureSection load='5c2d' size='340' side='right' caption='[[5c2d]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
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<StructureSection load='5c2d' size='340' side='right'caption='[[5c2d]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5c2d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C2D FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5c2d]] 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=5C2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C2D 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=CA:CALCIUM+ION'>CA</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]] 1.59&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4idh|4idh]], [[5c10|5c10]], [[5c12|5c12]], [[5c15|5c15]], [[5c2f|5c2f]]</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=CA:CALCIUM+ION'>CA</scene></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=5c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c2d OCA], [http://pdbe.org/5c2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c2d RCSB], [http://www.ebi.ac.uk/pdbsum/5c2d PDBsum]</span></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=5c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c2d OCA], [https://pdbe.org/5c2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c2d RCSB], [https://www.ebi.ac.uk/pdbsum/5c2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c2d 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/Q716H3_BPSFV Q716H3_BPSFV]
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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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
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</div>
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*[[Terminase 3D Structures|Terminase 3D Structures]]
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<div class="pdbe-citations 5c2d" 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: Tang, L]]
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[[Category: Large Structures]]
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[[Category: Zhao, H]]
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[[Category: Shigella virus Sf6]]
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[[Category: Metal binding protein]]
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[[Category: Tang L]]
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[[Category: Metal ion]]
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[[Category: Zhao H]]
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[[Category: Nuclease domain]]
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Current revision

K428A mutant gp2c of large terminase subunit from bacteriophage sf6 with calcium

PDB ID 5c2d

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