2qzy

From Proteopedia

(Difference between revisions)

Current revision

The structure of chicken mitochondrial PEPCK in complex with PEP

Structural highlights

2qzy is a 2 chain structure with sequence from Gallus gallus. This structure supersedes the now removed PDB entry 2fag. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

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

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.

Structural insights into the mechanism of PEPCK catalysis.,Holyoak T, Sullivan SM, Nowak T Biochemistry. 2006 Jul 11;45(27):8254-63. PMID:16819824^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Holyoak T, Sullivan SM, Nowak T. Structural insights into the mechanism of PEPCK catalysis. Biochemistry. 2006 Jul 11;45(27):8254-63. PMID:16819824 doi:10.1021/bi060269g

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2qzy"

Categories: Gallus gallus | Large Structures | Holyoak T | Nowak T | Sullivan SM

@@ Line 1: / Line 1: @@
 ==The structure of chicken mitochondrial PEPCK in complex with PEP==
-<StructureSection load='2qzy' size='340' side='right' caption='[[2qzy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2qzy' size='340' side='right'caption='[[2qzy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qzy]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QZY FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=20S:BETA-D-FRUCTOFURANOSYL+6-O-OCTANOYL-ALPHA-D-GLUCOPYRANOSIDE'>20S</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2faf|2faf]], [[2fah|2fah]]</td></tr>
+<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>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=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>
-<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=2qzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qzy OCA], [http://pdbe.org/2qzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qzy RCSB], [http://www.ebi.ac.uk/pdbsum/2qzy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qzy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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.
 == 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/qz/2qzy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qz/2qzy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 29: @@
 </div>
 <div class="pdbe-citations 2qzy" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phosphoenolpyruvate carboxykinase 3D structures|Phosphoenolpyruvate carboxykinase 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 37: @@
 </StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Holyoak, T]]
+[[Category: Large Structures]]
-[[Category: Nowak, T]]
+[[Category: Holyoak T]]
-[[Category: Sullivan, S M]]
+[[Category: Nowak T]]
-[[Category: Decarboxylase]]
+[[Category: Sullivan SM]]
-[[Category: Gluconeogenesis]]
-[[Category: Gtp-binding]]
-[[Category: Kinase]]
-[[Category: Lyase]]
-[[Category: Manganese]]
-[[Category: Mitochondrion]]
-[[Category: Nucleotide-binding]]
-[[Category: Pepck]]
-[[Category: Transit peptide]]

2qzy

From Proteopedia

Current revision

The structure of chicken mitochondrial PEPCK in complex with PEP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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