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

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

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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: https://doi.org/10.1002/pro.525
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
183Escherichia coliMutation(s): 1 
Find proteins for P45395 (Escherichia coli (strain K12))
Explore P45395 
Go to UniProtKB:  P45395
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45395
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.86α = 90
b = 67.43β = 106.94
c = 82.17γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description