2XHZ

Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing the Active Site of the Sugar Isomerase Domain from E. Coli Arabinose-5-Phosphate Isomerase Via X-Ray Crystallography.

Gourlay, L.J.Sommaruga, S.Nardini, M.Sperandeo, P.Deho, G.Polissi, A.Bolognesi, M.

(2010) Protein Sci. 19: 2430

  • DOI: 10.1002/pro.525

  • PubMed Abstract: 
  • Lipopolysaccharide (LPS) biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multidrug-resistant bacteria. A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomera ...

    Lipopolysaccharide (LPS) biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multidrug-resistant bacteria. A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. API is composed of two main domains: an N-terminal sugar isomerase domain (SIS) and a pair of cystathionine-β-synthase domains of unknown function. As the three-dimensional structure of an enzyme is a prerequisite for the rational development of novel inhibitors, we present here the crystal structure of the SIS domain of a catalytic mutant (K59A) of E. coli D-arabinose-5-phosphate isomerase at 2.6-Å resolution. Our structural analyses and comparisons made with other SIS domains highlight several potentially important active site residues. In particular, the crystal structure allowed us to identify a previously unpredicted His residue (H88) located at the mouth of the active site cavity as a possible catalytic residue. On the basis of such structural data, subsequently supported by biochemical and mutational experiments, we confirm the catalytic role of H88, which appears to be a generally conserved residue among two-domain isomerases.


    Organizational Affiliation

    Dipartimento di Scienze Biomolecolari e Biotecnologie, and CIMAINA, Università di Milano, Via Celoria 26, Milano 20133, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ARABINOSE 5-PHOSPHATE ISOMERASE
A, B, C, D
183Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: kdsD (yrbH)
EC: 5.3.1.13
Find proteins for P45395 (Escherichia coli (strain K12))
Go to UniProtKB:  P45395
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.860α = 90.00
b = 67.430β = 106.94
c = 82.170γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance