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PDBsum entry 2gac
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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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Crystal structures of flavobacterium glycosylasparaginase. An n-Terminal nucleophile hydrolase activated by intramolecular proteolysis.
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Authors
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H.C.Guo,
Q.Xu,
D.Buckley,
C.Guan.
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Ref.
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J Biol Chem, 1998,
273,
20205-20212.
[DOI no: ]
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PubMed id
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Abstract
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Glycosylasparaginase (GA) is a member of a novel family of N-terminal
nucleophile hydrolases that catalytically use an N-terminal residue as both a
polarizing base and a nucleophile. These enzymes are activated from a single
chain precursor by intramolecular autoproteolysis to yield the N-terminal
nucleophile. A deficiency of GA results in the human genetic disorder known as
aspartylglycosaminuria. In this study, we report the crystal structure of
recombinant GA from Flavobacterium meningosepticum. Similar to the human
structure, the bacterial GA forms an alphabetabetaalpha sandwich. However, some
significant differences are observed between the Flavobacterium and human
structures. The active site of Flavobacterium glycosylasparaginase is in an open
conformation when compared with the human structure. We also describe the
structure of a mutant wherein the N-terminal nucleophile Thr152 is substituted
by a cysteine. In the bacterial GA crystals, we observe a heterotetrameric
structure similar to that found in the human structure, as well as that observed
in solution for eukaryotic glycosylasparaginases. The results confirm the
suitability of the bacterial enzyme as a model to study the consequences of
mutations in aspartylglycosaminuria patients. They also suggest that further
studies are necessary to understand the detail mechanism of this enzyme. The
presence of the heterotetrameric structure in the crystals is significant
because dimerization of precursors has been suggested in the human enzyme to be
a prerequisite to trigger autoproteolysis.
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Figure 1.
Fig. 1. The structure of glycosylasparaginase from F.
meningosepticum. a, stereo ribbon representation of the
Flavobacterium GA structure. One heterodimer is shown with a-
(red) and b-subunits (green). The active site is at top center
of the structure toward the viewer and around the N-terminal end
of the b-subunit (green) (labeled Nb in light blue). b, stereo
diagram of C  traces of
Flavobacterium GA. c, stereo diagram of C traces of
Flavobacterium (dark blue) and human (gray) GA. Superimposition
is based on all common main chain atoms (excluding
insertions/deletions). The residues labeled are in
Flavobacterium sequence number.
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Figure 4.
Fig. 4. Stereo view of the active site of
glycosylasparaginase. a, stereo view of superimposition of the
active sites between Flavobacterium (shown according to atom
type: yellow for carbons, blue for nitrogens, and red for
oxygens) and human (shown in gray) GA. Also shown is aspartate
in the human enzyme/product structure (13). Dashed lines
correspond to the hydrogen bonds described in the human
structure. b, the same stereo view of active site in the T152C
mutant. The color scheme is the same as the wild type in (a),
except that sulfur of the thiol group is shown in green.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1998,
273,
20205-20212)
copyright 1998.
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