1KYH

Structure of Bacillus subtilis YxkO, a Member of the UPF0031 Family and a Putative Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.

Zhang, R.Grembecka, J.Vinokour, E.Collart, F.Dementieva, I.Minor, W.Joachimiak, A.

(2002) J.Struct.Biol. 139: 161-170


  • PubMed Abstract: 
  • We determined the 1.6-A resolution crystal structure of a conserved hypothetical 29.9-kDa protein from the SIGY-CYDD intergenic region encoded by a Bacillus subtilis open reading frame in the YXKO locus. YXKO homologues are broadly distributed and ar ...

    We determined the 1.6-A resolution crystal structure of a conserved hypothetical 29.9-kDa protein from the SIGY-CYDD intergenic region encoded by a Bacillus subtilis open reading frame in the YXKO locus. YXKO homologues are broadly distributed and are by and large described as proteins with unknown function. The YXKO protein has an alpha/beta fold and shows high structural homology to the members of a ribokinase-like superfamily. However, YXKO is the only member of this superfamily known to form tetramers. Putative binding sites for adenosine triphosphate (ATP), a substrate, and Mg(2+)-binding sites were revealed in the structure of the protein, based on high structural similarity to ATP-dependent members of the superfamily. Two adjacent monomers contribute residues to the active site. The crystal structure provides valuable information about the YXKO protein's tertiary and quaternary structure, the biochemical function of YXKO and its homologues, and the evolution of its ribokinase-like superfamily.


    Organizational Affiliation

    Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region
A
276Bacillus subtilis (strain 168)Gene Names: nnrD (yxkO)
EC: 4.2.1.136
Find proteins for P94368 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P94368
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.228 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.900α = 90.00
b = 91.900β = 90.00
c = 170.506γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-14
    Type: Initial release
  • Version 1.1: 2007-11-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description