1rr2: Difference between revisions

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OCA

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-[[Image:1rr2.gif|left|200px]]<br /><applet load="1rr2" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1rr2, resolution 2.00&Aring;" />
-'''Propionibacterium shermanii transcarboxylase 5S subunit bound to 2-ketobutyric acid'''<br />
-==Overview==
+==Propionibacterium shermanii transcarboxylase 5S subunit bound to 2-ketobutyric acid==
-Transcarboxylase is a 1.2 million Dalton (Da) multienzyme complex from, Propionibacterium shermanii that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate to yield, propionyl-CoA and oxaloacetate. Crystal structures of the 5S metalloenzyme, subunit, which catalyzes the second carboxylation reaction, have been, solved in free form and bound to its substrate pyruvate, product, oxaloacetate, or inhibitor 2-ketobutyrate. The structure reveals a dimer, of beta(8)alpha(8) barrels with an active site cobalt ion coordinated by a, carbamylated lysine, except in the oxaloacetate complex in which the, product's carboxylate group serves as a ligand instead. 5S and human, pyruvate carboxylase (PC), an enzyme crucial to gluconeogenesis, catalyze, similar reactions. A 5S-based homology model of the PC carboxyltransferase, domain indicates a conserved mechanism and explains the molecular basis of, mutations in lactic acidemia. PC disease mutations reproduced in 5S result, in a similar decrease in carboxyltransferase activity and crystal, structures with altered active sites.
+<StructureSection load='1rr2' size='340' side='right'caption='[[1rr2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rr2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RR2 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2KT:2-KETOBUTYRIC+ACID'>2KT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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=1rr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rr2 OCA], [https://pdbe.org/1rr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rr2 RCSB], [https://www.ebi.ac.uk/pdbsum/1rr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rr2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/5S_PROFR 5S_PROFR] The 5S subunit specifically catalyzes the transfer of the carboxyl group from biotin of the 1.3S subunit to pyruvate to form oxaloacetate and 1.3S biotin.
+== 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/rr/1rr2_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=1rr2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Transcarboxylase is a 1.2 million Dalton (Da) multienzyme complex from Propionibacterium shermanii that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate to yield propionyl-CoA and oxaloacetate. Crystal structures of the 5S metalloenzyme subunit, which catalyzes the second carboxylation reaction, have been solved in free form and bound to its substrate pyruvate, product oxaloacetate, or inhibitor 2-ketobutyrate. The structure reveals a dimer of beta(8)alpha(8) barrels with an active site cobalt ion coordinated by a carbamylated lysine, except in the oxaloacetate complex in which the product's carboxylate group serves as a ligand instead. 5S and human pyruvate carboxylase (PC), an enzyme crucial to gluconeogenesis, catalyze similar reactions. A 5S-based homology model of the PC carboxyltransferase domain indicates a conserved mechanism and explains the molecular basis of mutations in lactic acidemia. PC disease mutations reproduced in 5S result in a similar decrease in carboxyltransferase activity and crystal structures with altered active sites.
-==About this Structure==
+Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.,Hall PR, Zheng R, Antony L, Pusztai-Carey M, Carey PR, Yee VC EMBO J. 2004 Sep 15;23(18):3621-31. Epub 2004 Aug 26. PMID:15329673<ref>PMID:15329673</ref>
-RR2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii] with CO and 2KT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Methylmalonyl-CoA_carboxytransferase Methylmalonyl-CoA carboxytransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.1 2.1.3.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RR2 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit., Hall PR, Zheng R, Antony L, Pusztai-Carey M, Carey PR, Yee VC, EMBO J. 2004 Sep 15;23(18):3621-31. Epub 2004 Aug 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15329673 15329673]
+</div>
-[[Category: Methylmalonyl-CoA carboxytransferase]]
+<div class="pdbe-citations 1rr2" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Propionibacterium freudenreichii subsp. shermanii]]
-[[Category: Single protein]]
+[[Category: Antony L]]
-[[Category: Antony, L.]]
+[[Category: Carey PR]]
-[[Category: Carey, P.R.]]
+[[Category: Hall PR]]
-[[Category: Hall, P.R.]]
+[[Category: Pusztai-Carey M]]
-[[Category: Pusztai-Carey, M.]]
+[[Category: Yee VC]]
-[[Category: Yee, V.C.]]
+[[Category: Zheng R]]
-[[Category: Zheng, R.]]
-[[Category: 2KT]]
-[[Category: CO]]
-[[Category: 2-ketobutyric acid]]
-[[Category: carbamylated lysine]]
-[[Category: cobalt]]
-[[Category: tim-barrel]]
-[[Category: transcarboxylase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:48:41 2007''