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| | ==Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate== | | ==Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate== |
| - | <StructureSection load='1ylh' size='340' side='right' caption='[[1ylh]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='1ylh' size='340' side='right'caption='[[1ylh]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ylh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Actsc Actsc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YLH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ylh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinobacillus_succinogenes Actinobacillus succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YLH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DT3:(2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1-SULFONATE'>DT3</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ygg|1ygg]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DT3:(2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1-SULFONATE'>DT3</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PCKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=67854 ACTSC])</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=1ylh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ylh OCA], [https://pdbe.org/1ylh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ylh RCSB], [https://www.ebi.ac.uk/pdbsum/1ylh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ylh ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </span></td></tr>
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| - | <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=1ylh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ylh OCA], [http://pdbe.org/1ylh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ylh RCSB], [http://www.ebi.ac.uk/pdbsum/1ylh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ylh ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q6W6X5_ACTSC Q6W6X5_ACTSC]] Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA (By similarity).[HAMAP-Rule:MF_00453] | + | [https://www.uniprot.org/uniprot/PCKA_ACTSZ PCKA_ACTSZ] Involved in gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Phosphoenolpyruvate carboxykinase|Phosphoenolpyruvate carboxykinase]] | + | *[[Phosphoenolpyruvate carboxykinase 3D structures|Phosphoenolpyruvate carboxykinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actsc]] | + | [[Category: Actinobacillus succinogenes]] |
| - | [[Category: Delbaere, L T]] | + | [[Category: Large Structures]] |
| - | [[Category: Laivenieks, M]] | + | [[Category: Delbaere LT]] |
| - | [[Category: Leduc, Y A]] | + | [[Category: Laivenieks M]] |
| - | [[Category: Prasad, L]] | + | [[Category: Leduc YA]] |
| - | [[Category: Zeikus, J G]] | + | [[Category: Prasad L]] |
| - | [[Category: Bound sulfhydrl reducing agent]]
| + | [[Category: Zeikus JG]] |
| - | [[Category: Disulphide bond]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Phosphoenolpyruvate carboxykinase]]
| + | |
| Structural highlights
1ylh is a 1 chain structure with sequence from Actinobacillus succinogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.7Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PCKA_ACTSZ Involved in gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Actinobacillus succinogenes can produce, via fermentation, high concentrations of succinate, an important industrial commodity. A key enzyme in this pathway is phosphoenolpyruvate carboxykinase (PCK), which catalyzes the production of oxaloacetate from phosphoenolpyruvate and carbon dioxide, with the concomitant conversion of adenosine 5'-diphosphate to adenosine 5'-triphosphate. 1.85 and 1.70 A resolution structures of the native and a pyruvate/Mn(2+)/phosphate complex have been solved, respectively. The structure of the complex contains sulfhydryl reducing agents covalently bound to three cysteine residues via disulfide bonds. One of these cysteine residues (Cys285) is located in the active-site cleft and may be analogous to the putative reactive cysteine of PCK from Trypanosoma cruzi. Cys285 is also part of a previously unreported conserved motif comprising residues 280-287 and containing the pattern NXEXGXY(/F)A(/G); this new motif appears to have a structural role in stabilizing and positioning side chains that bind substrates and metal ions. The first few residues of this motif connect the two domains of the enzyme and a fulcrum point appears to be located near Asn280. In addition, an active-site Asp residue forms two coordinate bonds with the Mn(2+) ion present in the structure of the complex in a symmetrical bidentate manner, unlike in other PCK structures that contain a manganese ion.
Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif.,Leduc YA, Prasad L, Laivenieks M, Zeikus JG, Delbaere LT Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):903-12. Epub 2005, Jun 24. PMID:15983413[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Leduc YA, Prasad L, Laivenieks M, Zeikus JG, Delbaere LT. Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif. Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):903-12. Epub 2005, Jun 24. PMID:15983413 doi:10.1107/S0907444905008723
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