4zni: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Thermus Phage P74-26 Large Terminase ATPase domain (I 2 3 space group)==
-<StructureSection load='4zni' size='340' side='right' caption='[[4zni]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='4zni' size='340' side='right'caption='[[4zni]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zni]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZNI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zni]] 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=4ZNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZNI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.097&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4znj|4znj]], [[4znk|4znk]], [[4znl|4znl]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=4zni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zni OCA], [http://pdbe.org/4zni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zni RCSB], [http://www.ebi.ac.uk/pdbsum/4zni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zni 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=4zni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zni OCA], [https://pdbe.org/4zni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zni RCSB], [https://www.ebi.ac.uk/pdbsum/4zni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zni 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 package their genomes into procapsids using an ATPase machine that is among the most powerful known biological motors. However, how this motor couples ATP hydrolysis to DNA translocation is still unknown. Here, we introduce a model system with unique properties for studying motor structure and mechanism. We describe crystal structures of the packaging motor ATPase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. We also identify the arginine finger residue that catalyzes ATP hydrolysis in a neighboring motor subunit, illustrating that previous models for motor structure need revision. Our findings allow us to derive a structural model for the motor ring, which we validate using small-angle X-ray scattering and comparisons with previously published data. We illustrate the model's predictive power by identifying the motor's DNA-binding and assembly motifs. Finally, we integrate our results to propose a mechanistic model for DNA translocation by this molecular machine.
-Structure and mechanism of the ATPase that powers viral genome packaging.,Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):E3792-9. doi:, 10.1073/pnas.1506951112. Epub 2015 Jul 6. PMID:26150523<ref>PMID:26150523</ref>
+==See Also==
+*[[Terminase 3D Structures|Terminase 3D Structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4zni" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Duffy, C M]]
+[[Category: Large Structures]]
-[[Category: Hayes, J A]]
+[[Category: Thermus virus P74-26]]
-[[Category: Hilbert, B J]]
+[[Category: Duffy CM]]
-[[Category: Kelch, B A]]
+[[Category: Hayes JA]]
-[[Category: Sankaran, B]]
+[[Category: Hilbert BJ]]
-[[Category: Stone, N P]]
+[[Category: Kelch BA]]
-[[Category: Dna translocation]]
+[[Category: Sankaran B]]
-[[Category: Viral protein]]
+[[Category: Stone NP]]