2fpm: Difference between revisions

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-{{Seed}}
-[[Image:2fpm.png|left|200px]]
-<!--
+==RadA recombinase in complex with AMP-PNP and high concentration of K+==
-The line below this paragraph, containing "STRUCTURE_2fpm", creates the "Structure Box" on the page.
+<StructureSection load='2fpm' size='340' side='right'caption='[[2fpm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2fpm]] 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=1z4d 1z4d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2fpm|  PDB=2fpm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpm OCA], [https://pdbe.org/2fpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpm RCSB], [https://www.ebi.ac.uk/pdbsum/2fpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpm 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/2fpm_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=2fpm 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 AMP-PNP and high concentration of K+===
+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 2fpm" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16229465}}, adds the Publication Abstract to the page
+*[[Resolvase 3D structures|Resolvase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16229465 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16229465}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-FPM 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 [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1z4d 1z4d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPM OCA].
-==Reference==
-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: 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 Mon Jul 28 04:33:54 2008''