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| | <StructureSection load='1kc7' size='340' side='right'caption='[[1kc7]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='1kc7' size='340' side='right'caption='[[1kc7]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1kc7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteroides_symbiosus"_stevens_1956 "bacteroides symbiosus" stevens 1956]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KC7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1kc7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KC7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPR:PHOSPHONOPYRUVATE'>PPR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dik|1dik]], [[1kbl|1kbl]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPR:PHOSPHONOPYRUVATE'>PPR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PPDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1512 "Bacteroides symbiosus" Stevens 1956])</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=1kc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc7 OCA], [https://pdbe.org/1kc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kc7 RCSB], [https://www.ebi.ac.uk/pdbsum/1kc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc7 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/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1kc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc7 OCA], [http://pdbe.org/1kc7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kc7 RCSB], [http://www.ebi.ac.uk/pdbsum/1kc7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PPDK_CLOSY PPDK_CLOSY]] Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis. | + | [https://www.uniprot.org/uniprot/PPDK_CLOSY PPDK_CLOSY] Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacteroides symbiosus stevens 1956]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyruvate, phosphate dikinase]]
| + | [[Category: Chen CC]] |
| - | [[Category: Chen, C C]] | + | [[Category: Herzberg O]] |
| - | [[Category: Herzberg, O]] | + | [[Category: Howard A]] |
| - | [[Category: Howard, A]] | + | |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Phosphonopyruvate inhibitor]]
| + | |
| - | [[Category: Phosphotransferase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PPDK_CLOSY Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.
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
Crystals of pyruvate phosphate dikinase in complex with a substrate analogue inhibitor, phosphonopyruvate (K(i) = 3 microM), have been obtained in the presence of Mg(2+). The structure has been determined and refined at 2.2 A resolution, revealing that the Mg(2+)-bound phosphonopyruvate binds in the alpha/beta-barrel's central channel, at the C-termini of the beta-strands. The mode of binding resembles closely the previously proposed PEP substrate binding mode, inferred by the homology of the structure (but not sequence homology) to pyruvate kinase. Kinetic analysis of site-directed mutants, probing residues involved in inhibitor binding, showed that all mutations resulted in inactivation, confirming the key role that these residues play in catalysis. Comparison between the structure of the PPDK-phosphonopyruvate complex and the structures of two complexes of pyruvate kinase, one with Mg(2+)-bound phospholactate and the other with Mg(2+)-oxalate and ATP, revealed that the two enzymes share some key features that facilitate common modes of substrate binding. There are also important structural differences; most notably, the machinery for acid/base catalysis is different.
Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis.,Herzberg O, Chen CC, Liu S, Tempczyk A, Howard A, Wei M, Ye D, Dunaway-Mariano D Biochemistry. 2002 Jan 22;41(3):780-7. PMID:11790099[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Herzberg O, Chen CC, Liu S, Tempczyk A, Howard A, Wei M, Ye D, Dunaway-Mariano D. Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis. Biochemistry. 2002 Jan 22;41(3):780-7. PMID:11790099
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