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PDBsum entry 4my4
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PDB id:
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Isomerase
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Title:
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Crystal structure of phosphoglycerate mutase from staphylococcus aureus.
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Structure:
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2,3-bisphosphoglycerate-independent phosphoglycerate mutase. Chain: a. Fragment: unp residues 3-505. Synonym: bpg-independent pgam, phosphoglyceromutase, ipgm. Engineered: yes
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Source:
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Staphylococcus aureus subsp. Aureus. Organism_taxid: 93061. Strain: nctc8325. Gene: gpmi, saouhsc_00798. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.00Å
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R-factor:
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0.167
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R-free:
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0.216
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Authors:
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A.Roychowdhury,A.Kundu,A.Gujar,M.Bose,A.K.Das
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Key ref:
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A.Roychowdhury
et al.
(2015).
Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism.
Febs J,
282,
1097-1110.
PubMed id:
DOI:
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Date:
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27-Sep-13
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Release date:
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16-Oct-13
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PROCHECK
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Headers
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References
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Q2G029
(Q2G029_STAA8) -
2,3-bisphosphoglycerate-independent phosphoglycerate mutase from Staphylococcus aureus (strain NCTC 8325 / PS 47)
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Seq:
Struc:
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505 a.a.
503 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.5.4.2.12
- phosphoglycerate mutase (2,3-diphosphoglycerate-independent).
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Reaction:
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(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate
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2-phospho-D-glycerate
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=
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3-phospho-D-glycerate
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Cofactor:
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Cobalt cation or Mn(2+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Febs J
282:1097-1110
(2015)
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PubMed id:
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Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism.
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A.Roychowdhury,
A.Kundu,
M.Bose,
A.Gujar,
S.Mukherjee,
A.K.Das.
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ABSTRACT
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Cofactor-independent phosphoglycerate mutase (iPGM), an important enzyme in
glycolysis and gluconeogenesis, catalyses the isomerization of 2- and
3-phosphoglycerates by an Mn(2+) -dependent phospho-transfer mechanism via a
phospho-enzyme intermediate. Crystal structures of bi-domain iPGM from
Staphylococcus aureus, together with substrate-bound forms, have revealed a new
conformation of the enzyme, representing an intermediate state of domain
movement. The substrate-binding site and the catalytic site are present in two
distinct domains in the intermediate form. X-ray crystallography complemented by
simulated dynamics has enabled delineation of the complete catalytic cycle,
which includes binding of the substrate, followed by its positioning into the
catalytic site, phospho-transfer and finally product release. The present work
describes a novel mechanism of domain movement controlled by a hydrophobic patch
that is exposed on domain closure and acts like a spring to keep the protein in
open conformation. Domain closing occurs after substrate binding, and is
essential for phospho-transfer, whereas the open conformation is a prerequisite
for efficient substrate binding and product dissociation. A new model of
catalysis has been proposed by correlating the hinge-bending motion with the
phospho-transfer mechanism.
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