1TZ3

crystal structure of aminoimidazole riboside kinase complexed with aminoimidazole riboside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.str.2004.07.020
  • Primary Citation of Related Structures:  

  • 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 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative sugar kinase
A, B
339Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
EC: 2.7.1.4, 3.6.1.26
Find proteins for Q8ZKR2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZKR2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
AIS
Query on AIS

Download SDF File 
Download CCD File 
A
5-AMINOIMIDAZOLE RIBONUCLEOSIDE
C8 H13 N3 O4
NKYAAYKKNSYIIW-XVFCMESISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 135.851α = 90.00
b = 54.098β = 90.00
c = 89.796γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance