2vhc: Difference between revisions

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OCA

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-[[Image:2vhc.jpg|left|200px]]<br /><applet load="2vhc" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2vhc, resolution 2.35&Aring;" />
-'''P4 PROTEIN FROM BACTERIOPHAGE PHI12 N234G MUTANT IN COMPLEX WITH AMPCPP AND MN'''<br />
-==About this Structure==
+==P4 PROTEIN FROM BACTERIOPHAGE PHI12 N234G mutant in complex with AMPCPP and MN==
-VHC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_phi12 Pseudomonas phage phi12] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=APC:'>APC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Apc Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Mn Binding Site For Chain A'>AC2</scene>, <scene name='pdbsite=AC3:Apc Binding Site For Chain B'>AC3</scene>, <scene name='pdbsite=AC4:Mn Binding Site For Chain B'>AC4</scene>, <scene name='pdbsite=AC5:Apc Binding Site For Chain C'>AC5</scene> and <scene name='pdbsite=AC6:Mn Binding Site For Chain C'>AC6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHC OCA].
+<StructureSection load='2vhc' size='340' side='right'caption='[[2vhc]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2vhc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_phage_phi12 Pseudomonas phage phi12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2vhc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhc OCA], [https://pdbe.org/2vhc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhc RCSB], [https://www.ebi.ac.uk/pdbsum/2vhc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q94M05_9VIRU Q94M05_9VIRU]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The P4 protein of bacteriophage varphi12 is a hexameric molecular motor closely related to superfamily 4 helicases. P4 converts chemical energy from ATP hydrolysis into mechanical work, to translocate single-stranded RNA into a viral capsid. The molecular basis of mechanochemical coupling, i.e. how small approximately 1 A changes in the ATP-binding site are amplified into nanometer scale motion along the nucleic acid, is not understood at the atomic level. Here we study in atomic detail the mechanochemical coupling using structural and biochemical analyses of P4 mutants. We show that a conserved region, consisting of superfamily 4 helicase motifs H3 and H4 and loop L2, constitutes the moving lever of the motor. The lever tip encompasses an RNA-binding site that moves along the mechanical reaction coordinate. The lever is flanked by gamma-phosphate sensors (Asn-234 and Ser-252) that report the nucleotide state of neighboring subunits and control the lever position. Insertion of an arginine finger (Arg-279) into the neighboring catalytic site is concomitant with lever movement and commences ATP hydrolysis. This ensures cooperative sequential hydrolysis that is tightly coupled to mechanical motion. Given the structural conservation, the mutated residues may play similar roles in other hexameric helicases and related molecular motors.
+Structural Basis of Mechanochemical Coupling in a Hexameric Molecular Motor.,Kainov DE, Mancini EJ, Telenius J, Lisal J, Grimes JM, Bamford DH, Stuart DI, Tuma R J Biol Chem. 2008 Feb 8;283(6):3607-3617. Epub 2007 Dec 5. PMID:18057007<ref>PMID:18057007</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vhc" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas phage phi12]]
-[[Category: Single protein]]
+[[Category: Bamford DH]]
-[[Category: Bamford, D.H.]]
+[[Category: Grimes JM]]
-[[Category: Grimes, J.M.]]
+[[Category: Kainov DE]]
-[[Category: Kainov, D.E.]]
+[[Category: Lisal J]]
-[[Category: Lisal, J.]]
+[[Category: Mancini EJ]]
-[[Category: Mancini, E.J.]]
+[[Category: Stuart DI]]
-[[Category: Stuart, D.I.]]
+[[Category: Telenius J]]
-[[Category: Telenius, J.]]
+[[Category: Tuma R]]
-[[Category: Tuma, R.]]
-[[Category: APC]]
-[[Category: MN]]
-[[Category: hexameric helicase]]
-[[Category: hydrolase]]
-[[Category: molecular motor]]
-[[Category: non-hydrolysable atp analogue]]
-[[Category: packaging atpase]]
-[[Category: virus dsrna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:53:37 2008''