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PDBsum entry 1zdf
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References listed in PDB file
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Key reference
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Title
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Requirements for catalysis in mammalian glycogenin.
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Authors
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T.D.Hurley,
S.Stout,
E.Miner,
J.Zhou,
P.J.Roach.
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Ref.
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J Biol Chem, 2005,
280,
23892-23899.
[DOI no: ]
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PubMed id
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Abstract
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Glycogenin is a glycosyltransferase that functions as the autocatalytic
initiator for the synthesis of glycogen in eukaryotic organisms. Prior
structural work identified the determinants responsible for the recognition and
binding of UDP-glucose and the catalytic manganese ion and implicated two
aspartic acid residues in the reaction mechanism for self-glucosylation. We
examined the effects of substituting asparagine and serine for the aspartic acid
residues at positions 159 and 162. We also examined whether the truncation of
the protein at residue 270 (delta270) was compatible with its structural
integrity and its functional role as the initiator for glycogen synthesis. The
truncated form of the enzyme was indistinguishable from the wild-type enzyme by
all measures of activity and could support glycogen accumulation in a
glycogenin-deficient yeast strain. Substitution of aspartate 159 by either
serine or asparagine eliminated self-glucosylation and reduced
trans-glucosylation activity by at least 260-fold but only reduced UDP-glucose
hydrolytic activity by 4-14-fold. Substitution of aspartate 162 by either serine
or asparagine eliminated self-glucosylation activity and reduced UDP-glucose
hydrolytic activity by at least 190-fold. The trans-glucosylation of maltose was
reduced to undetectable levels in the asparagine 162 mutant, whereas the serine
162 enzyme showed only an 18-30-fold reduction in its ability to
trans-glucosylate maltose. These data support a role for aspartate 162 in the
chemical step for the glucosyltransferase reaction and a role for aspartate 159
in binding and activating the acceptor molecule.
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Figure 1.
FIG. 1. JZ4-a cells stained for glycogen accumulation using
iodine vapor. A, JZ4-a cells transformed only with wild-type
glycogenin-1. B, JZ4-a cells transformed only with 194F
glycogenin-1. C, JZ4-a cells transformed with both
194F-glycogenin-1 and  271-103A glycogenin-1.
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Figure 2.
FIG. 2. Subunit relationships among glycogenin crystal
forms. A, tetrameric association formed by crystallographic
contacts between the dimers that comprise the asymmetric unit in
the 270 crystals. Each
subunit is colored differently, and the position of Tyr-194 in
each subunit is highlighted using purple space-filling atoms,
and the position of the bound UDP molecules is highlighted using
blue space-filling atoms. B, alignment of the dimer formed by
one of the crystallographic axes in the I222 space group (red)
with the dimer of the 270 enzyme that
comprises the asymmetric unit of the P6[4] space group (yellow).
For this figure only the respective "A" subunits were aligned.
The red arrow indicates the amount of additional rotation
required to align the "B" subunits using the molecules oriented
in this manner. Figure was prepared using the programs MOLSCRIPT
(38) and Raster3D (39, 40).
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The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2005,
280,
23892-23899)
copyright 2005.
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Secondary reference #1
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Title
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Crystal structure of the autocatalytic initiator of glycogen biosynthesis, Glycogenin.
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Authors
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B.J.Gibbons,
P.J.Roach,
T.D.Hurley.
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Ref.
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J Mol Biol, 2002,
319,
463-477.
[DOI no: ]
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PubMed id
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Figure 7.
Figure 7. Glycogenin dimer ribbons diagram with a-helices
colored blue and green, b-sheets colored red and yellow, and
coils colored gray. UDP-glucose molecules and Tyr194 side-chains
are shown as ball-and-stick models and Mn2+ is colored magenta.
The distances between the C1'' atom of the glucose in
UDP-glucose and the Tyr194 hydroxyls are indicated with arrows.
This Figure was generated using SwissPdb Viewer[54] and rendered
using POV-Ray for Windows (downloaded from: www.povray.org).
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Figure 8.
Figure 8. (a) A stereoview of the cis peptide bond between
Glu118 and Leu119 is shown in a refined 2F[o] -F[c] simulated
annealing omit map contoured at 1.0s in which the contents of
the Figure were omitted from the structure factor calculations.
(b). A stereo view showing an F[o] -F[c] difference density map
contoured at 3.0s for the peptide bond between Glu118 and Leu119
refined in the trans conformation. The aligned cis conformation
is shown in gold for reference. (c) The cis peptide bond and
surrounding residues are shown, in stereo, as ball-and-stick
models. The amino acid residues interacting with Glu118 and
Leu119 are labeled. The helix between Phe170 and Asp162 is shown
as a green ribbon. These Figures were generated using SwissPdb
Viewer[54] and rendered using POV-Ray for Windows (downloaded
from: www.povray.org).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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