1DIL

SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EPANA INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

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

  • 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 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.


    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, Crystallization and Preliminary Crystallographic Study of Neuraminidase from Vibrio Cholerae and Salmonella Typhimurium Lt2
      Taylor, G., Vimr, E., Garman, E., Laver, G.
      (1992) J Mol Biol 226: 1287
    • Phosphonic-Acid Analogues of the N-Acetyl-2-Deoxyneuraminic Acids: Synthesis and Inhibition of Vibrio Cholerae Sialidase
      Wallimann, K., Vasella, A.
      (1990) Helv Chim Acta 73: 1359

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIALIDASEA381Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: nanHSTM0928
EC: 3.2.1.18
Find proteins for P29768 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P29768 
Go to UniProtKB:  P29768
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EQP
Query on EQP

Download Ideal Coordinates CCD File 
B [auth A](1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol
C10 H20 N O9 P
QITAGYVZDNZULE-IHICSVBISA-N
 Ligand Interaction
AXP
Query on AXP

Download Ideal Coordinates CCD File 
C [auth A](1S)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol
C10 H20 N O9 P
QITAGYVZDNZULE-HDBWYCHPSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.4α = 90
b = 82.3β = 90
c = 91.7γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary