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PDBsum entry 1qxr
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural evidence for a hydride transfer mechanism of catalysis in phosphoglucose isomerase from pyrococcus furiosus.
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Authors
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M.K.Swan,
J.T.Solomons,
C.C.Beeson,
T.Hansen,
P.Schönheit,
C.Davies.
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Ref.
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J Biol Chem, 2003,
278,
47261-47268.
[DOI no: ]
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PubMed id
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Abstract
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In the Euryarchaeota species Pyrococcus furiosus and Thermococcus litoralis,
phosphoglucose isomerase (PGI) activity is catalyzed by an enzyme unrelated to
the well known family of PGI enzymes found in prokaryotes, eukaryotes, and some
archaea. We have determined the crystal structure of PGI from Pyrococcus
furiosus in native form and in complex with two active site ligands,
5-phosphoarabinonate and gluconate 6-phosphate. In these structures, the metal
ion, which in vivo is presumed to be Fe2+, is located in the core of the cupin
fold and is immediately adjacent to the C1-C2 region of the ligands, suggesting
that Fe2+ is involved in catalysis rather than serving a structural role. The
active site contains a glutamate residue that contacts the substrate, but,
because it is also coordinated to the metal ion, it is highly unlikely to
mediate proton transfer in a cis-enediol mechanism. Consequently, we propose a
hydride shift mechanism of catalysis. In this mechanism, Fe2+ is responsible for
proton transfer between O1 and O2, and the hydride shift between C1 and C2 is
favored by a markedly hydrophobic environment in the active site. The absence of
any obvious enzymatic machinery for catalyzing ring opening of the sugar
substrates suggests that pyrococcal PGI has a preference for straight chain
substrates and that metabolism in extreme thermophiles may use sugars in both
ring and straight chain forms.
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Figure 4.
FIG. 4. The structure of the PfPGI in complex with PAB at
1.7 Å resolution. a, stereo view showing PAB bound to the
active site region of PfPGI. Monomer B of the dimer is shown,
but the contacts are essentially the same in monomer A. The
electron density is a F[o] - F[c] difference map calculated from
the final coordinates refined in the absence of ligand and thus
represents unbiased density of PAB. The side chains of those
residues surrounding the ligand are shown in ball-and-stick form
in which carbons are yellow, oxygens are red, and nitrogens are
blue. The metal ion atom, denoted M, is shown as an orange
sphere, and water molecules are shown as red spheres. Potential
hydrogen bonding and coordination contacts are shown as dashed
lines. The figure was produced using PyMOL (www.pymol.org) (32).
b, diagram of the contacts made between PAB and the enzyme in
which the distances are shown in Ångstroms. The inhibitor
is colored green.
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Figure 7.
FIG. 7. A catalytic mechanism for phosphoglucose isomerase
from P. furiosus, shown here in the glucose 6-phosphate to
fructose 6-phosphate direction. The substrate binds as the
straight form of G6P, and O1 and O2 displace both water
molecules from the coordination shell around Fe^2+. By
withdrawing electron density from O2, Fe^2+ facilitates the
movement of a proton from O2 to O1, creating a carbocation at
C1. An atom of hydrogen in the form of a hydride then shifts
from C2 to C1. A lone pair of electrons from O2 moves to form a
double bond between O2 and C2, thus creating F6P. When the
product leaves the active site, water molecules again occupy the
coordination positions left vacant by O1 and O2. Note that,
although Glu-97 is shown in this diagram, it does not play a
direct role in this proposed mechanism of catalysis. Its role
appears to be to counteract the positive charge of the inferred
Fe^2+ ion and it does not mediate proton transfer.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
47261-47268)
copyright 2003.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray diffraction analysis of phosphoglucose isomerase from pyrococcus furiosus.
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Authors
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M.K.Swan,
T.Hansen,
P.Schönheit,
C.Davies.
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Ref.
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Protein Pept Lett, 2003,
10,
517-520.
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PubMed id
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