PDBsum entry 1dil

Go to PDB code: 
protein ligands metals links
Glycosidase PDB id
Protein chain
381 a.a. *
Waters ×226
* Residue conservation analysis
PDB id:
Name: Glycosidase
Title: Sialidase from salmonella typhimurium complexed with apana a inhibitors
Structure: Sialidase. Chain: a. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Variant: ta263, prototroph. Gene: nanh. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: residue met 1 was excised by escherichia col
1.90Å     R-factor:   0.187    
Authors: E.F.Garman,S.C.Crennell,E.R.Vimr,W.G.Laver,G.L.Taylor
Key ref:
S.J.Crennell et al. (1996). The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution. J Mol Biol, 259, 264-280. PubMed id: 8656428 DOI: 10.1006/jmbi.1996.0318
23-Apr-96     Release date:   07-Dec-96    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P29768  (NANH_SALTY) -  Sialidase
382 a.a.
381 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1006/jmbi.1996.0318 J Mol Biol 259:264-280 (1996)
PubMed id: 8656428  
The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution.
S.J.Crennell, E.F.Garman, C.Philippon, A.Vasella, W.G.Laver, E.R.Vimr, G.L.Taylor.
The structure of Salmonella typhimurium LT2 neuraminidase (STNA) is reported here to a resolution of 1.6 angstroms together with the structures of three complexes of STNA with different inhibitors. The first is 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (Neu5Ac2en or DANA), the second and third are phosphonate derivatives of N-acetyl-neuraminic acid (NANA) which have phosphonate groups at the C2 position equatorial (ePANA) and axial (aPANA) to the plane of the sugar ring. The complex structures are at resolutions of 1.6 angstroms, 1.6 angstroms and 1.9 angstroms, respectively. These analyses show the STNA active site to be topologically inflexible and the interactions to be dominated by the arginine triad, with the pyranose rings of the inhibitors undergoing distortion to occupy the space available. Solvent structure differs only around the third phosphonate oxygen, which attracts a potassium ion. The STNA structure is topologically identical to the previously reported influenza virus neuraminidase structures, although very different in detail; the root-mean-square (r.m.s) deviation for 210 C alpha positions considered equivalent is 2.28 angstroms (out of a total of 390 residues in influenza and 381 in STNA). The active site residues are more highly conserved, in that both the viral and bacterial structures contain an arginine triad, a hydrophobic pocket, a tyrosine and glutamic acid residue at the base of the site and a potential proton-donating aspartic acid. However, differences in binding to O4 and to the glycerol side-chain may reflect the different kinetics employed by the two enzymes.
  Selected figure(s)  
Figure 2.
Figure 2. Stereo views of (a) the STNA C a trace (which has every tenth C a atom numbered) and (b) the B/Beijing monomer C a trace in the same orientation. The regions of the molecules which are within 1.5 Å in this superimposition are coloured red, the rest, black. A DANA molecule marks the position of the active site.
Figure 3.
Figure 3. Stereo views of (a) the S. typhimurium neuraminidase and (b) the B/Beijing influenza neuraminidase active sites with the DANA molecule (light bonds) bound and active site water molecules drawn as two concentric circles. Hydrogen bonds are shown as broken lines.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 259, 264-280) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20978010 D.C.Watson, S.Leclerc, W.W.Wakarchuk, and N.M.Young (2011).
Enzymatic synthesis and properties of glycoconjugates with legionaminic acid as a replacement for neuraminic acid.
  Glycobiology, 21, 99.  
19564377 D.Parker, G.Soong, P.Planet, J.Brower, A.J.Ratner, and A.Prince (2009).
The NanA neuraminidase of Streptococcus pneumoniae is involved in biofilm formation.
  Infect Immun, 77, 3722-3730.  
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
16862214 G.Soong, A.Muir, M.I.Gomez, J.Waks, B.Reddy, P.Planet, P.K.Singh, Y.Kaneko, Y.Kanetko, M.C.Wolfgang, Y.S.Hsiao, L.Tong, and A.Prince (2006).
Bacterial neuraminidase facilitates mucosal infection by participating in biofilm production.
  J Clin Invest, 116, 2297-2305.  
16149103 L.Ying, and J.Gervay-Hague (2005).
One-bead-one-inhibitor-one-substrate screening of neuraminidase activity.
  Chembiochem, 6, 1857-1865.  
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
12732625 M.Wimmerova, E.Mitchell, J.F.Sanchez, C.Gautier, and A.Imberty (2003).
Crystal structure of fungal lectin: six-bladed beta-propeller fold and novel fucose recognition mode for Aleuria aurantia lectin.
  J Biol Chem, 278, 27059-27067.
PDB code: 1ofz
12557186 S.C.Lovell, I.W.Davis, W.B.Arendall, Bakker, J.M.Word, M.G.Prisant, J.S.Richardson, and D.C.Richardson (2003).
Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
  Proteins, 50, 437-450.  
12668670 S.Planque, H.Taguchi, G.Burr, G.Bhatia, S.Karle, Y.X.Zhou, Y.Nishiyama, and S.Paul (2003).
Broadly distributed chemical reactivity of natural antibodies expressed in coordination with specific antigen binding activity.
  J Biol Chem, 278, 20436-20443.  
11401983 B.H.Jost, J.G.Songer, and S.J.Billington (2001).
Cloning, expression, and characterization of a neuraminidase gene from Arcanobacterium pyogenes.
  Infect Immun, 69, 4430-4437.  
11746676 H.Kamei, K.Shimazaki, and Y.Nishi (2001).
Computational 3-D modeling and site-directed mutation of an antibody that binds Neu2en5Ac, a transition state analogue of a sialic acid.
  Proteins, 45, 285-296.  
11381099 M.J.Jedrzejas (2001).
Pneumococcal virulence factors: structure and function.
  Microbiol Mol Biol Rev, 65, 187.  
11308029 R.G.Kleineidam, S.Kruse, P.Roggentin, and R.Schauer (2001).
Elucidation of the role of functional amino acid residues of the small sialidase from Clostridium perfringens by site-directed mutagenesis.
  Biol Chem, 382, 313-319.  
10619840 A.Buschiazzo, G.A.Tavares, O.Campetella, S.Spinelli, M.L.Cremona, G.París, M.F.Amaya, A.C.Frasch, and P.M.Alzari (2000).
Structural basis of sialyltransferase activity in trypanosomal sialidases.
  EMBO J, 19, 16-24.
PDB codes: 1mz5 1mz6
10801342 J.Yang, S.Schenkman, and B.A.Horenstein (2000).
Primary 13C and beta-secondary 2H KIEs for trans-sialidase. A snapshot of nucleophilic participation during catalysis.
  Biochemistry, 39, 5902-5910.  
11092845 S.Mizan, A.Henk, A.Stallings, M.Maier, and M.D.Lee (2000).
Cloning and characterization of sialidases with 2-6' and 2-3' sialyl lactose specificity from Pasteurella multocida.
  J Bacteriol, 182, 6874-6883.  
9733752 R.Amino, R.M.Porto, R.Chammas, M.I.Egami, and S.Schenkman (1998).
Identification and characterization of a sialidase released by the salivary gland of the hematophagous insect Triatoma infestans.
  J Biol Chem, 273, 24575-24582.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
9241431 C.Chothia, T.Hubbard, S.Brenner, H.Barns, and A.Murzin (1997).
Protein folds in the all-beta and all-alpha classes.
  Annu Rev Biophys Biomol Struct, 26, 597-627.  
9342319 J.N.Varghese, P.M.Colman, A.van Donkelaar, T.J.Blick, A.Sahasrabudhe, and J.L.McKimm-Breschkin (1997).
Structural evidence for a second sialic acid binding site in avian influenza virus neuraminidases.
  Proc Natl Acad Sci U S A, 94, 11808-11812.
PDB code: 1mwe
  9278056 T.F.Smith, L.Lo Conte, J.Bienkowska, C.Gaitatzes, R.G.Rogers, and R.Lathrop (1997).
Current limitations to protein threading approaches.
  J Comput Biol, 4, 217-225.  
8994884 G.Taylor (1996).
Sialidases: structures, biological significance and therapeutic potential.
  Curr Opin Struct Biol, 6, 830-837.  
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.