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PDBsum entry 1n1v
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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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The high resolution structures of free and inhibitor-Bound trypanosoma rangeli sialidase and its comparison with t. Cruzi trans-Sialidase.
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Authors
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M.F.Amaya,
A.Buschiazzo,
T.Nguyen,
P.M.Alzari.
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Ref.
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J Mol Biol, 2003,
325,
773-784.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the recombinant Trypanosoma rangeli sialidase (TrSA) has been
determined at 1.6A resolution, and the structures of its complexes with the
transition state analog inhibitor 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid
(DANA), Neu-5-Ac-thio-alpha(2,3)-galactoside (NATG) and N-acetylneuraminic acid
(NANA) have been determined at 1.64A, 2.1A and 2.85A, respectively. The 3D
structure of TrSA is essentially identical to that of the natural enzyme, except
for the absence of covalently attached sugar at five distinct N-glycosylation
sites. The protein exhibits a topologically rigid active site architecture that
is unaffected by ligand binding. The overall binding of DANA to the active site
cleft is similar to that observed for other viral and bacterial sialidases,
dominated by the interactions of the inhibitor carboxylate with the conserved
arginine triad. However, the interactions of the other pyranoside ring
substituents (hydroxyl, N-acetyl and glycerol moieties) differ between
trypanosomal, bacterial and viral sialidases, providing a structural basis for
specific inhibitor design. Sialic acid is found to bind the enzyme with the
sugar ring in a distorted (half-chair or boat) conformation and the 2-OH
hydroxyl group at hydrogen bonding distance of the carboxylate of Asp60,
substantiating a direct catalytic role for this residue. A detailed comparison
of TrSA with the closely related structure of T.cruzi trans-sialidase (TcTS)
reveals a highly conserved catalytic center, where subtle structural differences
account for strikingly different enzymatic activities and inhibition properties.
The structure of TrSA in complex with NATG shows the active site cleft occupied
by a smaller compound which could be identified as DANA, probably the product of
a hydrolytic side reaction. Indeed, TrSA (but not TcTS) was found to cleave O
and S-linked sialylated substrates, further stressing the functional differences
between trypanosomal sialidases and trans-sialidases.
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Figure 7.
Figure 7. Electron density (2Fo 2 Fc) contoured at 1.2s
showing the bound NANA molecule.
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Figure 8.
Figure 8. Simplified view show-
ing the hydrogen bonding inter-
actions of the ligand with the Arg
triad and the catalytic residue
Asp60. (a) A sulfate molecule sub-
stitutes the carboxylate group of
sialic acid in unliganded TrSA, and
interacts with Asp60 through two
water molecules. (b) Same view in
the TrSA -- DANA complex and (c)
in the TrSA -- NANA complex.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
325,
773-784)
copyright 2003.
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Secondary reference #1
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Title
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Structural basis of sialyltransferase activity in trypanosomal sialidases.
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Authors
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A.Buschiazzo,
G.A.Tavares,
O.Campetella,
S.Spinelli,
M.L.Cremona,
G.París,
M.F.Amaya,
A.C.Frasch,
P.M.Alzari.
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Ref.
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EMBO J, 2000,
19,
16-24.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3 Structure of TrSA in complex with DANA. (A) Final
electron density map at 2.9 Å resolution (contoured at 1.5
 ).
(B) Top view of the active site pocket with the bound inhibitor
(in yellow). (C) Scheme showing enzyme–inhibitor hydrogen
bonding interactions.
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Figure 5.
Figure 5 The active site cleft of trypanosomal sialidases. (A)
Structure of the TrSA–inhibitor complex colored according to
charge. (B) Model of TcTS with bound sialic acid. Amino acid
differences between TrSA and TcTS at the molecular surface
(colored in red) involve potential substrate-contacting residues
Ser120-Tyr, Gln284-Pro, Gly249-Tyr, Asp363-Glu and Phe59-Asn.
Putative binding sites for the sialic acid donor and acceptor
substrates, respectively, close to the aromatic side chains of
Trp313 and Tyr120 are indicated by dashed arrows (see the text
for details).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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