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| | ==Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxalate== | | ==Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxalate== |
| - | <StructureSection load='4mfd' size='340' side='right' caption='[[4mfd]], [[Resolution|resolution]] 2.55Å' scene=''> | + | <StructureSection load='4mfd' size='340' side='right'caption='[[4mfd]], [[Resolution|resolution]] 2.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mfd]] 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=4MFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MFD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mfd]] 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=4MFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MFD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mfe|4mfe]], [[4loc|4loc]], [[4jx5|4jx5]], [[4jx4|4jx4]], [[2qf7|2qf7]]</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=4mfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mfd OCA], [https://pdbe.org/4mfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mfd RCSB], [https://www.ebi.ac.uk/pdbsum/4mfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mfd ProSAT]</span></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=4mfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mfd OCA], [http://pdbe.org/4mfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mfd RCSB], [http://www.ebi.ac.uk/pdbsum/4mfd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mfd 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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| | </div> | | </div> |
| | <div class="pdbe-citations 4mfd" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4mfd" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Pyruvate carboxylase 3D structures|Pyruvate carboxylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __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: Maurice, M St]] | + | [[Category: StMaurice M]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
4mfd 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.
| | Method: | X-ray diffraction, Resolution 2.55Å |
| 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- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on alpha-keto acid substrates.
Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs.,Lietzan AD, St Maurice M Biochem Biophys Res Commun. 2013 Oct 22. pii: S0006-291X(13)01738-5. doi:, 10.1016/j.bbrc.2013.10.066. PMID:24157795[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lietzan AD, St Maurice M. Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs. Biochem Biophys Res Commun. 2013 Oct 22. pii: S0006-291X(13)01738-5. doi:, 10.1016/j.bbrc.2013.10.066. PMID:24157795 doi:http://dx.doi.org/10.1016/j.bbrc.2013.10.066
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