3QDK

Structural insight on mechanism and diverse substrate selection strategy of ribulokinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.

Agarwal, R., Burley, S.K., Swaminathan, S.

(2012) Proteins 80: 261-268

  • DOI: 10.1002/prot.23202

  • PubMed Abstract: 

    • The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosph ...

    The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k(cat) values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified (447)GGLPQK(452) as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment.

    Organizational Affiliation: 

    Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulokinase
A, B, C, D
572Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 0 
Gene Names: araB
EC: 2.7.1.16
Find proteins for Q9KBQ3 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KBQ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QDK
Query on QDK
Download SDF File 
Download CCD File 
A
L-ribulose
C5 H10 O5
ZAQJHHRNXZUBTE-UCORVYFPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.683α = 90.00
b = 88.840β = 92.75
c = 230.525γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
SHARPphasing
CCP4refinement
SHELXDphasing
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-28
    Type: Database references
  • Version 1.3: 2011-12-28
    Type: Database references