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Isomerase, hydrolase
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PDB id
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1yjx
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Contents |
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* Residue conservation analysis
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PDB id:
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Isomerase, hydrolase
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Title:
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Crystal structure of human b type phosphoglycerate mutase
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Structure:
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Phosphoglycerate mutase 1. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: phosphoglycerate mutase isozyme b, pgam-b, bpg- dependent pgam 1. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Dimer (from
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Resolution:
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2.80Å
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R-factor:
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0.233
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R-free:
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0.272
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Authors:
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Y.Wang,Z.Wei,L.Liu,W.Gong
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Key ref:
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Y.Wang
et al.
(2005).
Crystal structure of human B-type phosphoglycerate mutase bound with citrate.
Biochem Biophys Res Commun,
331,
1207-1215.
PubMed id:
DOI:
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Date:
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16-Jan-05
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Release date:
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17-May-05
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PROCHECK
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Headers
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References
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P18669
(PGAM1_HUMAN) -
Phosphoglycerate mutase 1
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Seq:
Struc:
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254 a.a.
245 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 2:
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E.C.3.1.3.13
- Bisphosphoglycerate phosphatase.
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Reaction:
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2,3-bisphospho-D-glycerate + H2O = 3-phospho-D-glycerate + phosphate
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2,3-bisphospho-D-glycerate
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+
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H(2)O
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=
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3-phospho-D-glycerate
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+
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phosphate
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Enzyme class 3:
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E.C.5.4.2.1
- Phosphoglycerate mutase.
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Reaction:
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2-phospho-D-glycerate = 3-phospho-D-glycerate
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2-phospho-D-glycerate
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=
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3-phospho-D-glycerate
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Enzyme class 4:
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E.C.5.4.2.4
- Bisphosphoglycerate mutase.
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Reaction:
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3-phospho-D-glyceroyl phosphate = 2,3-bisphospho-D-glycerate
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3-phospho-D-glyceroyl phosphate
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=
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2,3-bisphospho-D-glycerate
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytosol
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1 term
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Biological process
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metabolic process
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5 terms
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Biochemical function
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catalytic activity
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8 terms
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DOI no:
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Biochem Biophys Res Commun
331:1207-1215
(2005)
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PubMed id:
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Crystal structure of human B-type phosphoglycerate mutase bound with citrate.
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Y.Wang,
Z.Wei,
L.Liu,
Z.Cheng,
Y.Lin,
F.Ji,
W.Gong.
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ABSTRACT
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The B-type cofactor-dependent phosphoglycerate mutase (dPGM-B) catalyzes the
interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and
gluconeogenesis pathways using 2,3-bisphosphoglycerate as the cofactor. The
crystal structures of human dPGM-B bound with citrate were determined in two
crystal forms. These structures reveal a dimerization mode conserved in both of
dPGM and BPGM (bisphosphoglycerate mutase), based on which a dPGM/BPGM
heterodimer structure is proposed. Structural comparison supports that the
conformational changes of residues 13-21 and 98-117 determine PGM/BPGM activity
differences. The citrate-binding mode suggests a substrate-binding model,
consistent with the structure of Escherichia coli dPGM/vanadate complex. A
chloride ion was found in the center of the dimer, providing explanation for the
contribution of chloride ion to dPGM activities. Based on the structural
information, the possible reasons for the deficient human dPGM mutations found
in some patients are also discussed.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Dai,
L.Finci,
C.Zhang,
S.Lahiri,
G.Zhang,
E.Peisach,
K.N.Allen,
and
D.Dunaway-Mariano
(2009).
Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis.
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Biochemistry, 48,
1984-1995.
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PDB code:
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M.J.Evans,
G.M.Morris,
J.Wu,
A.J.Olson,
E.J.Sorensen,
and
B.F.Cravatt
(2007).
Mechanistic and structural requirements for active site labeling of phosphoglycerate mutase by spiroepoxides.
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Mol Biosyst, 3,
495-506.
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H.A.Watkins,
and
E.N.Baker
(2006).
Structural and functional analysis of Rv3214 from Mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase.
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J Bacteriol, 188,
3589-3599.
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PDB code:
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N.K.Lokanath,
and
N.Kunishima
(2006).
Purification, crystallization and preliminary X-ray crystallographic analysis of the archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 62,
788-790.
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Y.Wang,
L.Liu,
Z.Wei,
Z.Cheng,
Y.Lin,
and
W.Gong
(2006).
Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.
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J Biol Chem, 281,
39642-39648.
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PDB codes:
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M.J.Evans,
A.Saghatelian,
E.J.Sorensen,
and
B.F.Cravatt
(2005).
Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling.
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Nat Biotechnol, 23,
1303-1307.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
