2qzy

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(New page: 200px<br /><applet load="2qzy" size="450" color="white" frame="true" align="right" spinBox="true" caption="2qzy, resolution 1.9&Aring;" /> '''The structure of chic...)
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[[Image:2qzy.jpg|left|200px]]<br /><applet load="2qzy" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2qzy, resolution 1.9&Aring;" />
 
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'''The structure of chicken mitochondrial PEPCK in complex with PEP'''<br />
 
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==Overview==
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==The structure of chicken mitochondrial PEPCK in complex with PEP==
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Phosphoenolpyruvate carboxykinase catalyzes the reversible decarboxylation, of oxaloacetic acid with the concomitant transfer of the gamma-phosphate, of GTP to form PEP and GDP as the first committed step of gluconeogenesis, and glyceroneogenesis. The three structures of the mitochondrial isoform, of PEPCK reported are complexed with Mn2+, Mn2+-PEP, or Mn2+-malonate-Mn2+, GDP and provide the first observations of the structure of the, mitochondrial isoform and insight into the mechanism of catalysis mediated, by this enzyme. The structures show the involvement of the hyper-reactive, cysteine (C307) in the coordination of the active site Mn2+. Upon, formation of the PEPCK-Mn2+-PEP or PEPCK-Mn2+-malonate-Mn2+ GDP complexes, C307 coordination is lost as the P-loop in which it resides adopts a, different conformation. The structures suggest that stabilization of the, cysteine-coordinated metal geometry holds the enzyme as a catalytically, incompetent metal complex and may represent a previously unappreciated, mechanism of regulation. A third conformation of the mobile P-loop in the, PEPCK-Mn2+-malonate-Mn2+ GDP complex demonstrates the participation of a, previously unrecognized, conserved serine residue (S305) in mediating, phosphoryl transfer. The ordering of the mobile active site lid in the, PEPCK-Mn2+-malonate-Mn2+ GDP complex yields the first observation of this, structural feature and provides additional insight into the mechanism of, phosphoryl transfer.
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<StructureSection load='2qzy' size='340' side='right'caption='[[2qzy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2qzy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fag 2fag]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QZY FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PRD_900043:octanoyl-sucrose,+esterificated+at+glucose+C6'>PRD_900043</scene>, <scene name='pdbligand=TQY:6-O-octanoyl-alpha-D-glucopyranose'>TQY</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qzy OCA], [https://pdbe.org/2qzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qzy RCSB], [https://www.ebi.ac.uk/pdbsum/2qzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qzy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PCKGM_CHICK PCKGM_CHICK] Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle. Facilitates the recycling of lactate carbon in the liver.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qz/2qzy_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2qzy ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Phosphoenolpyruvate carboxykinase catalyzes the reversible decarboxylation of oxaloacetic acid with the concomitant transfer of the gamma-phosphate of GTP to form PEP and GDP as the first committed step of gluconeogenesis and glyceroneogenesis. The three structures of the mitochondrial isoform of PEPCK reported are complexed with Mn2+, Mn2+-PEP, or Mn2+-malonate-Mn2+ GDP and provide the first observations of the structure of the mitochondrial isoform and insight into the mechanism of catalysis mediated by this enzyme. The structures show the involvement of the hyper-reactive cysteine (C307) in the coordination of the active site Mn2+. Upon formation of the PEPCK-Mn2+-PEP or PEPCK-Mn2+-malonate-Mn2+ GDP complexes, C307 coordination is lost as the P-loop in which it resides adopts a different conformation. The structures suggest that stabilization of the cysteine-coordinated metal geometry holds the enzyme as a catalytically incompetent metal complex and may represent a previously unappreciated mechanism of regulation. A third conformation of the mobile P-loop in the PEPCK-Mn2+-malonate-Mn2+ GDP complex demonstrates the participation of a previously unrecognized, conserved serine residue (S305) in mediating phosphoryl transfer. The ordering of the mobile active site lid in the PEPCK-Mn2+-malonate-Mn2+ GDP complex yields the first observation of this structural feature and provides additional insight into the mechanism of phosphoryl transfer.
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==About this Structure==
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Structural insights into the mechanism of PEPCK catalysis.,Holyoak T, Sullivan SM, Nowak T Biochemistry. 2006 Jul 11;45(27):8254-63. PMID:16819824<ref>PMID:16819824</ref>
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2QZY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with MN, PEP, EPE and 20S as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 2FAG. Active as [http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2QZY OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural insights into the mechanism of PEPCK catalysis., Holyoak T, Sullivan SM, Nowak T, Biochemistry. 2006 Jul 11;45(27):8254-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16819824 16819824]
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</div>
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[[Category: Gallus gallus]]
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<div class="pdbe-citations 2qzy" style="background-color:#fffaf0;"></div>
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[[Category: Phosphoenolpyruvate carboxykinase (GTP)]]
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[[Category: Single protein]]
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[[Category: Holyoak, T.]]
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[[Category: Nowak, T.]]
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[[Category: Sullivan, S.M.]]
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[[Category: 20S]]
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[[Category: EPE]]
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[[Category: MN]]
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[[Category: PEP]]
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[[Category: decarboxylase]]
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[[Category: gluconeogenesis]]
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[[Category: gtp-binding]]
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[[Category: kinase]]
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[[Category: lyase]]
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[[Category: manganese]]
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[[Category: mitochondrion]]
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[[Category: nucleotide-binding]]
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[[Category: pepck]]
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[[Category: transit peptide]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:56:27 2007''
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==See Also==
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*[[Phosphoenolpyruvate carboxykinase 3D structures|Phosphoenolpyruvate carboxykinase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Gallus gallus]]
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[[Category: Large Structures]]
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[[Category: Holyoak T]]
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[[Category: Nowak T]]
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[[Category: Sullivan SM]]

Current revision

The structure of chicken mitochondrial PEPCK in complex with PEP

PDB ID 2qzy

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