1on3
From Proteopedia
(Difference between revisions)
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<StructureSection load='1on3' size='340' side='right'caption='[[1on3]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='1on3' size='340' side='right'caption='[[1on3]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>[[1on3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1on3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii Propionibacterium freudenreichii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ON3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ON3 FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DXX:METHYLMALONIC+ACID'>DXX</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
- | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DXX:METHYLMALONIC+ACID'>DXX</scene>, <scene name='pdbligand=MCA:METHYLMALONYL-COENZYME+A'>MCA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr> | |
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1on3 OCA], [https://pdbe.org/1on3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1on3 RCSB], [https://www.ebi.ac.uk/pdbsum/1on3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1on3 ProSAT]</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=1on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1on3 OCA], [https://pdbe.org/1on3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1on3 RCSB], [https://www.ebi.ac.uk/pdbsum/1on3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1on3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
- | + | [https://www.uniprot.org/uniprot/12S_PROFR 12S_PROFR] The 12S subunit specifically catalyzes the transfer of the carboxyl group of methylmalonyl CoA to the biotin of the 1.3S subunit forming propanoyl-CoA and carboxylated 1.3S-biotin. | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=1on3 ConSurf]. | </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=1on3 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
- | <div style="background-color:#fffaf0;"> | ||
- | == Publication Abstract from PubMed == | ||
- | Transcarboxylase from Propionibacterium shermanii is a 1.2 MDa multienzyme complex that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate, yielding propionyl-CoA and oxaloacetate. The 1.9 A resolution crystal structure of the central 12S hexameric core, which catalyzes the first carboxylation reaction, has been solved bound to its substrate methylmalonyl-CoA. Overall, the structure reveals two stacked trimers related by 2-fold symmetry, and a domain duplication in the monomer. In the active site, the labile carboxylate group of methylmalonyl-CoA is stabilized by interaction with the N-termini of two alpha-helices. The 12S domains are structurally similar to the crotonase/isomerase superfamily, although only domain 1 of each 12S monomer binds ligand. The 12S reaction is similar to that of human propionyl-CoA carboxylase, whose beta-subunit has 50% sequence identity with 12S. A homology model of the propionyl-CoA carboxylase beta-subunit, based on this 12S crystal structure, provides new insight into the propionyl-CoA carboxylase mechanism, its oligomeric structure and the molecular basis of mutations responsible for enzyme deficiency in propionic acidemia. | ||
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- | Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core.,Hall PR, Wang YF, Rivera-Hainaj RE, Zheng X, Pustai-Carey M, Carey PR, Yee VC EMBO J. 2003 May 15;22(10):2334-47. PMID:12743028<ref>PMID:12743028</ref> | ||
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- | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
- | </div> | ||
- | <div class="pdbe-citations 1on3" style="background-color:#fffaf0;"></div> | ||
- | == References == | ||
- | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
- | [[Category: Bacterium acidi propionici a von freudenreich and orla-jensen 1907]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
- | [[Category: | + | [[Category: Propionibacterium freudenreichii]] |
- | [[Category: Carey | + | [[Category: Carey PR]] |
- | [[Category: Hall | + | [[Category: Hall PR]] |
- | [[Category: Pustai-Carey | + | [[Category: Pustai-Carey M]] |
- | [[Category: Rivera-Hainaj | + | [[Category: Rivera-Hainaj RE]] |
- | [[Category: Wang | + | [[Category: Wang Y-F]] |
- | [[Category: Yee | + | [[Category: Yee VC]] |
- | [[Category: Zheng | + | [[Category: Zheng X]] |
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Current revision
Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with methylmalonyl-coenzyme a and methylmalonic acid bound)
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