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PDBsum entry 1ffr
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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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High resolution structural analyses of mutant chitinase a complexes with substrates provide new insight into the mechanism of catalysis.
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Authors
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Y.Papanikolau,
G.Prag,
G.Tavlas,
C.E.Vorgias,
A.B.Oppenheim,
K.Petratos.
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Ref.
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Biochemistry, 2001,
40,
11338-11343.
[DOI no: ]
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PubMed id
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Abstract
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Chitinase A (ChiA) from the bacterium Serratia marcescens is a hydrolytic
enzyme, which cleaves beta-1,4-glycosidic bonds of the natural biopolymer chitin
to generate di-N-acetyl-chitobiose. The refined structure of ChiA at 1.55 A
shows that residue Asp313, which is located near the catalytic proton donor
residue Glu315, is found in two alternative conformations of equal occupancy. In
addition, the structures of the cocrystallized mutant proteins D313A, E315Q,
Y390F, and D391A with octa- or hexa-N-acetyl-glucosamine have been refined at
high resolution and the interactions with the substrate have been characterized.
The obtained results clearly show that the active site is a semiclosed tunnel.
Upon binding, the enzyme bends and rotates the substrate in the vicinity of the
scissile bond. Furthermore, the enzyme imposes a critical "chair" to "boat"
conformational change on the sugar residue bound to the -1 subsite. According to
our results, we suggest that residues Asp313 and Tyr390 along with Glu315 play a
central role in the catalysis. We propose that after the protonation of the
substrate glycosidic bond, Asp313 that interacts with Asp311 flips to its
alternative position where it interacts with Glu315 thus forcing the substrate
acetamido group of -1 sugar to rotate around the C2-N2 bond. As a result of
these structural changes, the water molecule that is hydrogen-bonded to Tyr390
and the NH of the acetamido group is displaced to a position that allows the
completion of hydrolysis. The presented results suggest a mechanism for ChiA
that modifies the earlier proposed "substrate assisted" catalysis.
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Secondary reference #1
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Title
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De novo purification scheme and crystallization conditions yield high-Resolution structures of chitinase a and its complex with the inhibitor allosamidin.
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Authors
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Y.Papanikolau,
G.Tavlas,
C.E.Vorgias,
K.Petratos.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
400-403.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 ChiA-allosamidin complex. (a) Stereoview of the C^  -atom
trace of the enzyme molecule (green) with the inhibitor (red)
bound to the active-site tunnel (PDB code [112]1ffq ). (b)
Allosamidin in the electron density of the weighted 2F[o] - F[c]
map contoured at 2 [113][sigma] (blue) and the neighbouring
residues of ChiA. (c) Close-up view of allosamidin bound to the
enzyme's active-site tunnel at subsites -1 to -3. The
allosamizoline moiety fits into a local well.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #2
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Title
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Crystal structure of a bacterial chitinase at 2.3 a resolution.
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Authors
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A.Perrakis,
I.Tews,
Z.Dauter,
A.B.Oppenheim,
I.Chet,
K.S.Wilson,
C.E.Vorgias.
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Ref.
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Structure, 1994,
2,
1169-1180.
[DOI no: ]
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PubMed id
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Figure 8.
Figure 8. Difference density (F[o]–F[c] , with phases from
the native model) clearly showing the bound NAG. The active-site
residues are shown. Density is contoured at the 4σ level. The
orientation of the ring is not clear, and it is modelled in the
most likely position according to chemical knowledge of the
reaction mechanism, as described in the text. The role of water
181 is unclear. It is presented here to show the interpretation
of this density. Figure drawn using O/OPLOT [39]. Figure 8.
Difference density (F[o]–F[c] , with phases from the native
model) clearly showing the bound NAG. The active-site residues
are shown. Density is contoured at the 4σ level. The
orientation of the ring is not clear, and it is modelled in the
most likely position according to chemical knowledge of the
reaction mechanism, as described in the text. The role of water
181 is unclear. It is presented here to show the interpretation
of this density. Figure drawn using O/OPLOT [[3]39].
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Figure 11.
Figure 11. Stereo representation of the active site of ChiA.
Carbons are drawn in black, oxygens in red and nitrogens in
blue. Details for the proposed mechanism are given in the text.
Figure 11. Stereo representation of the active site of ChiA.
Carbons are drawn in black, oxygens in red and nitrogens in
blue. Details for the proposed mechanism are given in the text.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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