2fpk: Difference between revisions

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-[[Image:2fpk.jpg|left|200px]]
- {{Structure
+==RadA recombinase in complex with ADP==
-|PDB= 2fpk |SIZE=350|CAPTION= <scene name='initialview01'>2fpk</scene>, resolution 2.10&Aring;
+<StructureSection load='2fpk' size='340' side='right'caption='[[2fpk]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> and <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>
+<table><tr><td colspan='2'>[[2fpk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanococcus_voltae Methanococcus voltae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1z4b 1z4b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPK FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-|GENE= RADA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2188 Methanococcus voltae])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2fpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpk OCA], [https://pdbe.org/2fpk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpk RCSB], [https://www.ebi.ac.uk/pdbsum/2fpk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RADA_METVO RADA_METVO] Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fpk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Members of a superfamily of RecA-like recombinases facilitate a central strand exchange reaction in the DNA repair process. Archaeal RadA and Rad51 and eukaryal Rad51 and meiosis-specific DMC1 form a closely related group of recombinases distinct from bacterial RecA. Nevertheless, all such recombinases share a conserved core domain which carries the ATPase site and putative DNA-binding sites. Here we present the crystal structure of an archaeal RadA from Methanococcus voltae (MvRadA) in complex with ADP and Mg2+ at 2.1 A resolution. The crystallized RadA-ADP filament has an extended helical pitch similar to those of previously determined structures in the presence of nonhydrolyzable ATP analogue AMP-PNP. Structural comparison reveals two recurrent conformations with an extensive allosteric effect spanning the ATPase site and the putative DNA-binding L2 region. Varied conformations of the L2 region also imply a dynamic nature of recombinase-bound DNA.
-'''RadA recombinase in complex with ADP'''
+Crystal structure of Methanococcus voltae RadA in complex with ADP: hydrolysis-induced conformational change.,Qian X, Wu Y, He Y, Luo Y Biochemistry. 2005 Oct 25;44(42):13753-61. PMID:16229465<ref>PMID:16229465</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2fpk" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Members of a superfamily of RecA-like recombinases facilitate a central strand exchange reaction in the DNA repair process. Archaeal RadA and Rad51 and eukaryal Rad51 and meiosis-specific DMC1 form a closely related group of recombinases distinct from bacterial RecA. Nevertheless, all such recombinases share a conserved core domain which carries the ATPase site and putative DNA-binding sites. Here we present the crystal structure of an archaeal RadA from Methanococcus voltae (MvRadA) in complex with ADP and Mg2+ at 2.1 A resolution. The crystallized RadA-ADP filament has an extended helical pitch similar to those of previously determined structures in the presence of nonhydrolyzable ATP analogue AMP-PNP. Structural comparison reveals two recurrent conformations with an extensive allosteric effect spanning the ATPase site and the putative DNA-binding L2 region. Varied conformations of the L2 region also imply a dynamic nature of recombinase-bound DNA.
+*[[Resolvase 3D structures|Resolvase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-FPK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanococcus_voltae Methanococcus voltae]. This structure supersedes the now removed PDB entry 1Z4B. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPK OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Crystal structure of Methanococcus voltae RadA in complex with ADP: hydrolysis-induced conformational change., Qian X, Wu Y, He Y, Luo Y, Biochemistry. 2005 Oct 25;44(42):13753-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16229465 16229465]
 [[Category: Methanococcus voltae]]
-[[Category: Single protein]]
+[[Category: He Y]]
-[[Category: He, Y.]]
+[[Category: Luo Y]]
-[[Category: Luo, Y.]]
+[[Category: Moya IA]]
-[[Category: Moya, I A.]]
+[[Category: Qian X]]
-[[Category: Qian, X.]]
+[[Category: Wu Y]]
-[[Category: Wu, Y.]]
-[[Category: ADP]]
-[[Category: K]]
-[[Category: MG]]
-[[Category: atpase]]
-[[Category: co-factor]]
-[[Category: potassium-dependence]]
-[[Category: protein-atp complex]]
-[[Category: rada/adp complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:06:53 2008''