1kbl: Difference between revisions
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< | ==PYRUVATE PHOSPHATE DIKINASE== | ||
<StructureSection load='1kbl' size='340' side='right'caption='[[1kbl]], [[Resolution|resolution]] 1.94Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1kbl]] 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=1KBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBL FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1kbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbl OCA], [https://pdbe.org/1kbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbl RCSB], [https://www.ebi.ac.uk/pdbsum/1kbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbl ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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 == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kbl_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=1kbl ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:11790099</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1kbl" style="background-color:#fffaf0;"></div> | |||
== | |||
==See Also== | ==See Also== | ||
*[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]] | *[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Chen | [[Category: Chen CC]] | ||
[[Category: Herzberg | [[Category: Herzberg O]] | ||
[[Category: Liu | [[Category: Liu S]] | ||
Latest revision as of 11:55, 16 August 2023
PYRUVATE PHOSPHATE DIKINASEPYRUVATE PHOSPHATE DIKINASE
Structural highlights
FunctionPPDK_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 PubMedCrystals 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 AlsoReferences |
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