5c2d: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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>
</td></tr><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>
</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>
<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>
<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>
<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>
== 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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5c2d" 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>

Latest revision as of 15:18, 6 March 2024

K428A mutant gp2c of large terminase subunit from bacteriophage sf6 with calciumK428A mutant gp2c of large terminase subunit from bacteriophage sf6 with calcium

Structural highlights

5c2d is a 1 chain structure with sequence from Shigella virus Sf6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.59Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q716H3_BPSFV

See Also

5c2d, resolution 1.59Å

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