6v2n: Difference between revisions
New page: '''Unreleased structure''' The entry 6v2n is ON HOLD Authors: Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D. Description: Crystal structure of E. coli phosph... |
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==Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys254Ser== | |||
<StructureSection load='6v2n' size='340' side='right'caption='[[6v2n]], [[Resolution|resolution]] 1.65Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6v2n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6cu4 6cu4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V2N 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]] 1.65Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6v2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v2n OCA], [https://pdbe.org/6v2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v2n RCSB], [https://www.ebi.ac.uk/pdbsum/6v2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v2n ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PCKA_ECOLI PCKA_ECOLI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Phosphoenolpyruvate carboxykinase (PEPCK) is a metabolic enzyme in the gluconeogenesis pathway, where it catalyzes the reversible conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) and CO2. The substrates for Escherichia coli PEPCK are OAA and MgATP, with Mn(2+) acting as a cofactor. Analysis of PEPCK structures have revealed amino acid residues involved in substrate/cofactor coordination during catalysis. METHODS: Key residues involved in coordinating the different substrates and cofactor bound to E. coli PEPCK were mutated. Purified mutant enzymes were used for kinetic assays. The structure of some mutant enzymes were determined using X-ray crystallography. RESULTS: Mutation of residues D269 and H232, which comprise part of the coordination sphere of Mn(2+), reduced kcat by 14-fold, and significantly increased the Km values for Mn(2+) and OAA. Mutation of K254 a key residue in the P-loop motif that interacts with MgATP, significantly elevated the Km value for MgATP and reduced kcat. R65 and R333 are key residues that interacts with OAA. The R65Q and R333Q mutations significantly increased the Km value for OAA and reduced kcat respectively. CONCLUSIONS: Our results show that mutation of residues involved in coordinating OAA, MgATP and Mn(2+) significantly reduce PEPCK activity. K254 plays an important role in phosphoryl transfer, while R333 is involved in both OAA decarboxylation and phosphoryl transfer by E. coli PEPCK. GENERAL SIGNIFICANCE: In higher organisms including humans, PEPCK helps to regulate blood glucose levels, hence PEPCK is a potential drug target for patients with non-insulin dependent diabetes mellitus. | |||
Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants.,Sokaribo A, Novakovski BAA, Cotelesage J, White AP, Sanders D, Goldie H Biochim Biophys Acta Gen Subj. 2020 Jan 3;1864(4):129517. doi:, 10.1016/j.bbagen.2020.129517. PMID:31911238<ref>PMID:31911238</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6v2n" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Goldie | ==See Also== | ||
[[Category: Novakovski | *[[Phosphoenolpyruvate carboxykinase 3D structures|Phosphoenolpyruvate carboxykinase 3D structures]] | ||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli]] | |||
[[Category: Large Structures]] | |||
[[Category: Cotelesage JH]] | |||
[[Category: Goldie H]] | |||
[[Category: Novakovski B]] | |||
[[Category: Sanders D]] | |||
[[Category: Sokaribo AS]] | |||
Latest revision as of 11:02, 11 October 2023
Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys254SerCrystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys254Ser
Structural highlights
FunctionPublication Abstract from PubMedBACKGROUND: Phosphoenolpyruvate carboxykinase (PEPCK) is a metabolic enzyme in the gluconeogenesis pathway, where it catalyzes the reversible conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) and CO2. The substrates for Escherichia coli PEPCK are OAA and MgATP, with Mn(2+) acting as a cofactor. Analysis of PEPCK structures have revealed amino acid residues involved in substrate/cofactor coordination during catalysis. METHODS: Key residues involved in coordinating the different substrates and cofactor bound to E. coli PEPCK were mutated. Purified mutant enzymes were used for kinetic assays. The structure of some mutant enzymes were determined using X-ray crystallography. RESULTS: Mutation of residues D269 and H232, which comprise part of the coordination sphere of Mn(2+), reduced kcat by 14-fold, and significantly increased the Km values for Mn(2+) and OAA. Mutation of K254 a key residue in the P-loop motif that interacts with MgATP, significantly elevated the Km value for MgATP and reduced kcat. R65 and R333 are key residues that interacts with OAA. The R65Q and R333Q mutations significantly increased the Km value for OAA and reduced kcat respectively. CONCLUSIONS: Our results show that mutation of residues involved in coordinating OAA, MgATP and Mn(2+) significantly reduce PEPCK activity. K254 plays an important role in phosphoryl transfer, while R333 is involved in both OAA decarboxylation and phosphoryl transfer by E. coli PEPCK. GENERAL SIGNIFICANCE: In higher organisms including humans, PEPCK helps to regulate blood glucose levels, hence PEPCK is a potential drug target for patients with non-insulin dependent diabetes mellitus. Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants.,Sokaribo A, Novakovski BAA, Cotelesage J, White AP, Sanders D, Goldie H Biochim Biophys Acta Gen Subj. 2020 Jan 3;1864(4):129517. doi:, 10.1016/j.bbagen.2020.129517. PMID:31911238[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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