PDBsum entry 1n1v

Go to PDB code: 
Top Page protein ligands links
Hydrolase PDB id
Protein chain
628 a.a. *
SO4 ×2
Waters ×295
* Residue conservation analysis

References listed in PDB file
Key reference
Title The high resolution structures of free and inhibitor-Bound trypanosoma rangeli sialidase and its comparison with t. Cruzi trans-Sialidase.
Authors M.F.Amaya, A.Buschiazzo, T.Nguyen, P.M.Alzari.
Ref. J Mol Biol, 2003, 325, 773-784. [DOI no: 10.1016/S0022-2836(02)01306-2]
PubMed id 12507479
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.
Figure 7.
Figure 7. Electron density (2Fo 2 Fc) contoured at 1.2s showing the bound NANA molecule.
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.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 325, 773-784) copyright 2003.
Secondary reference #1
Title Structural basis of sialyltransferase activity in trypanosomal sialidases.
Authors A.Buschiazzo, G.A.Tavares, O.Campetella, S.Spinelli, M.L.Cremona, G.París, M.F.Amaya, A.C.Frasch, P.M.Alzari.
Ref. EMBO J, 2000, 19, 16-24. [DOI no: 10.1093/emboj/19.1.16]
PubMed id 10619840
Full text Abstract
Figure 3.
Figure 3 Structure of TrSA in complex with DANA. (A) Final electron density map at 2.9 Šresolution (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.
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).
The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd
Go to PROCHECK summary