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PDBsum entry 1n1t

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Hydrolase PDB id
1n1t
Jmol
Contents
Protein chain
628 a.a. *
Ligands
SO4 ×2
DAN
Waters ×661
* Residue conservation analysis
PDB id:
1n1t
Name: Hydrolase
Title: Trypanosoma rangeli sialidase in complex with dana at 1.6 a
Structure: Sialidase. Chain: a. Fragment: residue 23-660. Engineered: yes
Source: Trypanosoma rangeli. Organism_taxid: 5698. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.174     R-free:   0.197
Authors: M.F.Amaya,A.Buschiazzo,T.Nguyen,P.M.Alzari
Key ref:
M.F.Amaya et al. (2003). The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase. J Mol Biol, 325, 773-784. PubMed id: 12507479 DOI: 10.1016/S0022-2836(02)01306-2
Date:
20-Oct-02     Release date:   07-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O44049  (O44049_TRYRA) -  Sialidase
Seq:
Struc:
 
Seq:
Struc:
660 a.a.
628 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.18  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     exo-alpha-(2->3)-sialidase activity     6 terms  

 

 
DOI no: 10.1016/S0022-2836(02)01306-2 J Mol Biol 325:773-784 (2003)
PubMed id: 12507479  
 
 
The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase.
M.F.Amaya, A.Buschiazzo, T.Nguyen, P.M.Alzari.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20511247 A.Albohy, M.D.Li, R.B.Zheng, C.Zou, and C.W.Cairo (2010).
Insight into substrate recognition and catalysis by the human neuraminidase 3 (NEU3) through molecular modeling and site-directed mutagenesis.
  Glycobiology, 20, 1127-1138.  
20645127 M.E.Giorgi, L.Ratier, R.Agusti, A.C.Frasch, and R.M.de Lederkremer (2010).
Synthesis of PEGylated lactose analogs for inhibition studies on T.cruzi trans-sialidase.
  Glycoconj J, 27, 549-559.  
19216574 O.Demir, and A.E.Roitberg (2009).
Modulation of catalytic function by differential plasticity of the active site: case study of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase.
  Biochemistry, 48, 3398-3406.  
  18765901 G.Xu, X.Li, P.W.Andrew, and G.L.Taylor (2008).
Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 772-775.
PDB codes: 2vvz 2w20
18949046 L.Ratier, M.Urrutia, G.Paris, L.Zarebski, A.C.Frasch, and F.A.Goldbaum (2008).
Relevance of the diversity among members of the Trypanosoma cruzi trans-sialidase family analyzed with camelids single-domain antibodies.
  PLoS ONE, 3, e3524.  
16298994 A.G.Watts, P.Oppezzo, S.G.Withers, P.M.Alzari, and A.Buschiazzo (2006).
Structural and kinetic analysis of two covalent sialosyl-enzyme intermediates on Trypanosoma rangeli sialidase.
  J Biol Chem, 281, 4149-4155.
PDB codes: 2a75 2ags 2fhr
16320365 S.W.Hinz, C.H.Doeswijk-Voragen, R.Schipperus, L.A.van den Broek, J.P.Vincken, and A.G.Voragen (2006).
Increasing the transglycosylation activity of alpha-galactosidase from Bifidobacterium adolescentis DSM 20083 by site-directed mutagenesis.
  Biotechnol Bioeng, 93, 122-131.  
15292273 A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
  J Biol Chem, 279, 44907-44914.
PDB codes: 1wd3 1wd4
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
15007099 E.R.Vimr, K.A.Kalivoda, E.L.Deszo, and S.M.Steenbergen (2004).
Diversity of microbial sialic acid metabolism.
  Microbiol Mol Biol Rev, 68, 132-153.  
15226294 I.Moustafa, H.Connaris, M.Taylor, V.Zaitsev, J.C.Wilson, M.J.Kiefel, M.von Itzstein, and G.Taylor (2004).
Sialic acid recognition by Vibrio cholerae neuraminidase.
  J Biol Chem, 279, 40819-40826.
PDB codes: 1w0o 1w0p
15130470 M.F.Amaya, A.G.Watts, I.Damager, A.Wehenkel, T.Nguyen, A.Buschiazzo, G.Paris, A.C.Frasch, S.G.Withers, and P.M.Alzari (2004).
Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.
  Structure, 12, 775-784.
PDB codes: 1s0i 1s0j 1s0k 2ah2
15016893 V.Zaitsev, M.von Itzstein, D.Groves, M.Kiefel, T.Takimoto, A.Portner, and G.Taylor (2004).
Second sialic acid binding site in Newcastle disease virus hemagglutinin-neuraminidase: implications for fusion.
  J Virol, 78, 3733-3741.
PDB codes: 1usr 1usx
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.