5tge: Difference between revisions

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 <StructureSection load='5tge' size='340' side='right'caption='[[5tge]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5tge]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bp742 Bp742]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TGE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5tge]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_virus_P74-26 Thermus virus P74-26]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TGE FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">P74p84 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=466052 BP742])</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]] 2.6&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5tge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tge OCA], [http://pdbe.org/5tge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tge RCSB], [http://www.ebi.ac.uk/pdbsum/5tge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tge 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=5tge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tge OCA], [https://pdbe.org/5tge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tge RCSB], [https://www.ebi.ac.uk/pdbsum/5tge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tge ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A7XXR1_BP742 A7XXR1_BP742] The terminase large subunit acts as an ATP driven molecular motor necessary for viral DNA translocation into empty capsids and as an endonuclease that cuts the viral genome to initiate and to end a packaging reaction. The terminase lies at a unique vertex of the procapsid and is composed of two subunits, a small terminase subunit involved in viral DNA recognition (packaging sequence), and a large terminase subunit possessing endonucleolytic and ATPase activities. Both terminase subunits heterooligomerize and are docked on the portal protein to form the packaging machine. The terminase large subunit exhibits endonuclease activity and cleaves the viral genome concatemer. Once the capsid is packaged with the DNA, the terminase complex is substituted by the tail.[HAMAP-Rule:MF_04146]
-Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA.
-The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain.,Hilbert BJ, Hayes JA, Stone NP, Xu RG, Kelch BA Nucleic Acids Res. 2017 Jan 12. pii: gkw1356. doi: 10.1093/nar/gkw1356. PMID:28082398<ref>PMID:28082398</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5tge" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Terminase|Terminase]]
+*[[Terminase 3D Structures|Terminase 3D Structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bp742]]
 [[Category: Large Structures]]
-[[Category: Hayes, J A]]
+[[Category: Thermus virus P74-26]]
-[[Category: Hilbert, B J]]
+[[Category: Hayes JA]]
-[[Category: Kelch, B A]]
+[[Category: Hilbert BJ]]
-[[Category: Stone, N P]]
+[[Category: Kelch BA]]
-[[Category: Nuclease]]
+[[Category: Stone NP]]
-[[Category: Viral protein]]