Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.99 kDa 
• Atom Count: 3149 
• Modelled Residue Count: 381 
• Deposited Residue Count: 381 
• Unique protein chains: 1

2SIL

THE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND ITS COMPLEX WITH A TRANSITION STATE ANALOGUE AT 1.6 ANGSTROMS RESOLUTION

• PDB DOI: 10.2210/pdb2SIL/pdb
• Entry: 2SIL supersedes: 1SIL

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): No 


• Deposited: 1994-07-13 Released: 1994-08-31 
• Deposition Author(s): Taylor, G.L., Crennell, S.J., Garman, E.F., Vimr, E.R., Laver, W.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Literature

The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution.

Crennell, S.J., Garman, E.F., Philippon, C., Vasella, A., Laver, W.G., Vimr, E.R., Taylor, G.L.

(1996) J Mol Biol 259: 264-280

• PubMed: 8656428 
• DOI: 10.1006/jmbi.1996.0318
• Primary Citation of Related Structures:  
  1DIL, 1DIM, 2SIL, 2SIM


• PubMed Abstract: 
  

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.

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Related Citations: 

• Crystal Structure of a Bacterial Sialidase (from Salmonella Typhimurium Lt2) Shows the Same Fold as an Influenza Virus Neuraminidase
  Crennell, S.J., Garman, E.F., Laver, W.G., Vimr, E.R., Taylor, G.L.
  (1993) Proc Natl Acad Sci U S A 90: 9852

• Purification, Crystallisation and Preliminary Crystallographic Study of Neuraminidase from Vibrio Cholerae and Salmonella Typhimurium
  Taylor, G.L., Vimr, E.R., Garman, E.F., Laver, W.G.
  (1992) J Mol Biol 226: 1287

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Organizational Affiliation: 

Department of Biochemistry, University of Bath, Claverton Down, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIALIDASE	A	381	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: PSX62 EC: 3.2.1.18
UniProt
Find proteins for P29768 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P29768  Go to UniProtKB:  P29768

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.5	α = 90
b = 82.5	β = 90
c = 91.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-07-13 
• Released Date: 1994-08-31 
Deposition Author(s): Taylor, G.L., Crennell, S.J., Garman, E.F., Vimr, E.R., Laver, W.G.
• This entry supersedes: 1SIL

Revision History  

• Version 1.0: 1994-08-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description