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| | ==Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin== | | ==Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin== |
| - | <StructureSection load='4m6v' size='340' side='right' caption='[[4m6v]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='4m6v' size='340' side='right'caption='[[4m6v]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4m6v]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhiec Rhiec]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M6V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4m6v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizobium_etli_CFN_42 Rhizobium etli CFN 42]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M6V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BYT:BIOCYTIN'>BYT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BYT:BIOCYTIN'>BYT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4m6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m6v OCA], [https://pdbe.org/4m6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m6v RCSB], [https://www.ebi.ac.uk/pdbsum/4m6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m6v ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4loc|4loc]], [[4jx5|4jx5]], [[4jx4|4jx4]], [[3tw6|3tw6]], [[2qf7|2qf7]], [[4mfd|4mfd]], [[4mfe|4mfe]], [[4mim|4mim]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyc, RHE_CH04002 ([http://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'>[http://en.wikipedia.org/wiki/Pyruvate_carboxylase Pyruvate carboxylase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4m6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m6v OCA], [http://pdbe.org/4m6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m6v RCSB], [http://www.ebi.ac.uk/pdbsum/4m6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m6v ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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] | + | [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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyruvate carboxylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Rhiec]] | + | [[Category: Rhizobium etli CFN 42]] |
| - | [[Category: Lietzan, A D]] | + | [[Category: Lietzan AD]] |
| - | [[Category: St Maurice, M]] | + | [[Category: StMaurice M]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
4m6v is a 4 chain structure with sequence from Rhizobium etli CFN 42. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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]
Publication Abstract from PubMed
Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. During catalysis, carboxybiotin is translocated to the carboxyltransferase domain where the carboxyl group is transferred to the acceptor substrate, pyruvate. Many studies on the carboxyltransferase domain of PC have demonstrated an enhanced oxaloacetate decarboxylation activity in the presence of oxamate and it has been shown that oxamate accepts a carboxyl group from carboxybiotin during oxaloacetate decarboxylation. The X-ray crystal structure of the carboxyltransferase domain from Rhizobium etli PC reveals that oxamate is positioned in the active site in an identical manner to the substrate, pyruvate, and kinetic data are consistent with the oxamate-stimulated decarboxylation of oxaloacetate proceeding through a simple ping-pong bi bi mechanism in the absence of the biotin carboxylase domain. Additionally, analysis of truncated PC enzymes indicates that the BCCP domain devoid of biotin does not contribute directly to the enzymatic reaction and conclusively demonstrates a biotin-independent oxaloacetate decarboxylation activity in PC. These findings advance the description of catalysis in PC and can be extended to the study of related biotin-dependent enzymes.
The role of biotin and oxamate in the carboxyl transferase reaction of pyruvate carboxylase.,Lietzan AD, Lin Y, St Maurice M Arch Biochem Biophys. 2014 Aug 23. pii: S0003-9861(14)00308-7. doi:, 10.1016/j.abb.2014.08.008. PMID:25157442[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lietzan AD, Lin Y, St Maurice M. The role of biotin and oxamate in the carboxyl transferase reaction of pyruvate carboxylase. Arch Biochem Biophys. 2014 Aug 23. pii: S0003-9861(14)00308-7. doi:, 10.1016/j.abb.2014.08.008. PMID:25157442 doi:http://dx.doi.org/10.1016/j.abb.2014.08.008
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