2qf7: Difference between revisions

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-{{Seed}}
-[[Image:2qf7.png|left|200px]]
-<!--
+==Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli==
-The line below this paragraph, containing "STRUCTURE_2qf7", creates the "Structure Box" on the page.
+<StructureSection load='2qf7' size='340' side='right'caption='[[2qf7]], [[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'>[[2qf7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhiec Rhiec]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QF7 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-{{STRUCTURE_2qf7|  PDB=2qf7  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyc ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=347834 RHIEC])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_carboxylase Pyruvate carboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.4.1.1 6.4.1.1] </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=2qf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qf7 OCA], [https://pdbe.org/2qf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qf7 RCSB], [https://www.ebi.ac.uk/pdbsum/2qf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qf7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/Q2K340_RHIEC Q2K340_RHIEC]] Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second (By similarity).[PIRNR:PIRNR001594]
+== 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/qf/2qf7_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=2qf7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biotin-dependent multifunctional enzymes carry out metabolically important carboxyl group transfer reactions and are potential targets for the treatment of obesity and type 2 diabetes. These enzymes use a tethered biotin cofactor to carry an activated carboxyl group between distantly spaced active sites. The mechanism of this transfer has remained poorly understood. Here we report the complete structure of pyruvate carboxylase at 2.0 angstroms resolution, which shows its domain arrangement. The structure, when combined with mutagenic analysis, shows that intermediate transfer occurs between active sites on separate polypeptide chains. In addition, domain rearrangements associated with activator binding decrease the distance between active-site pairs, providing a mechanism for allosteric activation. This description provides insight into the function of biotin-dependent enzymes and presents a new paradigm for multifunctional enzyme catalysis.
-===Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli===
+Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.,St Maurice M, Reinhardt L, Surinya KH, Attwood PV, Wallace JC, Cleland WW, Rayment I Science. 2007 Aug 24;317(5841):1076-9. PMID:17717183<ref>PMID:17717183</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17717183}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2qf7" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17717183 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17717183}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-QF7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhizobium_etli Rhizobium etli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QF7 OCA].
-==Reference==
-Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme., St Maurice M, Reinhardt L, Surinya KH, Attwood PV, Wallace JC, Cleland WW, Rayment I, Science. 2007 Aug 24;317(5841):1076-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17717183 17717183]
 [[Category: Pyruvate carboxylase]]
-[[Category: Rhizobium etli]]
+[[Category: Rhiec]]
-[[Category: Single protein]]
+[[Category: Maurice, M St]]
-[[Category: Maurice, M St.]]
+[[Category: Rayment, I]]
-[[Category: Rayment, I.]]
+[[Category: Surinya, K H]]
-[[Category: Surinya, K H.]]
 [[Category: Biotin-dependent]]
 [[Category: Ligase]]
 [[Category: Multi-domain]]
 [[Category: Multi-functional]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 16:47:25 2008''