Crystal structure of aminoimidazole riboside kinase from Salmonella enterica

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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Crystal Structure of an Aminoimidazole Riboside Kinase from Salmonella enterica; Implications for the Evolution of the Ribokinase Superfamily

Zhang, Y.Dougherty, M.Downs, D.M.Ealick, S.E.

(2004) Structure 12: 1809-1821

  • DOI: https://doi.org/10.1016/j.str.2004.07.020
  • Primary Citation of Related Structures:  
    1TYY, 1TZ3, 1TZ6

  • PubMed Abstract: 

    The crystal structures of a Salmonella enterica aminoimidazole riboside (AIRs) kinase, its complex with the substrate AIRs, and its complex with AIRs and an ATP analog were determined at 2.6 angstroms, 2.9 angstroms, and 2.7 angstroms, respectively. The product of the Salmonella-specific gene stm4066, AIRs kinase, is a homodimer with one active site per monomer. The core structure, consisting of an eight-stranded beta sheet flanked by eight alpha helices, indicates that AIRs kinase is a member of the ribokinase superfamily. Unlike ribokinase and adenosine kinase in this superfamily, AIRs kinase does not show significant conformational changes upon substrate binding. The active site is covered by a lid formed by residues 16-28 and 86-100. A comparison of the structure of AIRs kinase with other ribokinase superfamily members suggests that the active site lid and conformational changes that occur upon substrate binding may be advanced features in the evolution of the ribokinase superfamily.

  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative sugar kinase
A, B
339Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 4 
Gene Names: stm4066
Find proteins for Q8ZKR2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZKR2 
Go to UniProtKB:  Q8ZKR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZKR2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.43α = 90
b = 53.987β = 90
c = 89.485γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance