1rqb: Difference between revisions

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-[[Image:1rqb.gif|left|200px]]
- {{Structure
+==Propionibacterium shermanii transcarboxylase 5S subunit==
-|PDB= 1rqb |SIZE=350|CAPTION= <scene name='initialview01'>1rqb</scene>, resolution 1.90&Aring;
+<StructureSection load='1rqb' size='340' side='right'caption='[[1rqb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
+<table><tr><td colspan='2'>[[1rqb]] 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=1RQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RQB FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-|GENE= 5S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1752 Propionibacterium freudenreichii subsp. shermanii])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rqb OCA], [https://pdbe.org/1rqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rqb RCSB], [https://www.ebi.ac.uk/pdbsum/1rqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rqb ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1rqe|1RQE]], [[1rqh|1RQH]], [[1rr2|1RR2]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rqb OCA], [http://www.ebi.ac.uk/pdbsum/1rqb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rqb RCSB]</span>
+== 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 ==
-'''Propionibacterium shermanii transcarboxylase 5S subunit'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rq/1rqb_consurf.spt"</scriptWhenChecked>
-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.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-RQB is a [[Single protein]] structure of sequence from [http://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=1RQB OCA].
+</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=1rqb ConSurf].
+<div style="clear:both"></div>
-==Reference==
+__TOC__
-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://www.ncbi.nlm.nih.gov/pubmed/15329673 15329673]
+</StructureSection>
-[[Category: Methylmalonyl-CoA carboxytransferase]]
+[[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: carbamylated lysine]]
-[[Category: tim-barrel]]
-[[Category: transcarboxylase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:31:32 2008''