5m1k: Difference between revisions

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 ==Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Magnesium==
-<StructureSection load='5m1k' size='340' side='right' caption='[[5m1k]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+<StructureSection load='5m1k' size='340' side='right'caption='[[5m1k]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5m1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M1K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5m1k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_phage_G20c Thermus phage G20c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M1K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5m1f|5m1f]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<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=5m1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1k OCA], [http://pdbe.org/5m1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1k RCSB], [http://www.ebi.ac.uk/pdbsum/5m1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1k 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=5m1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1k OCA], [https://pdbe.org/5m1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m1k RCSB], [https://www.ebi.ac.uk/pdbsum/5m1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1k ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TERL_BPG20 TERL_BPG20]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+ High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism.
+Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.,Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA Nucleic Acids Res. 2017 Jan 18. pii: gkw1354. doi: 10.1093/nar/gkw1354. PMID:28100693<ref>PMID:28100693</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5m1k" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Terminase 3D Structures|Terminase 3D Structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Antson, A A]]
+[[Category: Large Structures]]
-[[Category: Blagova, E V]]
+[[Category: Thermus phage G20c]]
-[[Category: Chechik, M]]
+[[Category: Antson AA]]
-[[Category: Greive, S J]]
+[[Category: Blagova EV]]
-[[Category: Jenkins, H T]]
+[[Category: Chechik M]]
-[[Category: Xu, R G]]
+[[Category: Greive SJ]]
-[[Category: Large terminase]]
+[[Category: Jenkins HT]]
-[[Category: Nuclease domain]]
+[[Category: Xu RG]]
-[[Category: Viral protein]]