The structure and function of B. subtilis YkoF gene product: the complex with thiamin

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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The Structure and Ligand Binding Properties of the B.subtilis YkoF Gene Product, a Member of a Novel Family of Thiamin/HMP-binding Proteins

Devedjiev, Y.Surendranath, Y.Derewenda, U.Gabrys, A.Cooper, D.R.Zhang, R.G.Lezondra, L.Joachimiak, A.Derewenda, Z.S.

(2004) J Mol Biol 343: 395-406

  • DOI: https://doi.org/10.1016/j.jmb.2004.08.037
  • Primary Citation of Related Structures:  
    1S99, 1SBR

  • PubMed Abstract: 

    The crystal structure of the Bacillus subtilis YkoF gene product, a protein involved in the hydroxymethyl pyrimidine (HMP) salvage pathway, was solved by the multiwavelength anomalous dispersion (MAD) method and refined with data extending to 1.65 A resolution. The atomic model of the protein shows a homodimeric association of two polypeptide chains, each containing an internal repeat of a ferredoxin-like betaalphabetabetaalphabeta fold, as seen in the ACT and RAM-domains. Each repeat shows a remarkable similarity to two members of the COG0011 domain family, the MTH1187 and YBL001c proteins, the crystal structures of which were recently solved by the Northeast Structural Genomics Consortium. Two YkoF monomers form a tightly associated dimer, in which the amino acid residues forming the interface are conserved among family members. A putative small-ligand binding site was located within each repeat in a position analogous to the serine-binding site of the ACT-domain of the Escherichia coli phosphoglycerate dehydrogenase. Genetic data suggested that this could be a thiamin or HMP-binding site. Calorimetric data confirmed that YkoF binds two thiamin molecules with varying affinities and a thiamine-YkoF complex was obtained by co-crystallization. The atomic model of the complex was refined using data to 2.3 A resolution and revealed a unique H-bonding pattern that constitutes the molecular basis of specificity for the HMP moiety of thiamin.

  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908-0736, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
200Bacillus subtilisMutation(s): 2 
Gene Names: YkoF
Find proteins for O34911 (Bacillus subtilis (strain 168))
Explore O34911 
Go to UniProtKB:  O34911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34911
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
VIB PDBBind:  1SBR Kd: 1.00e+4 (nM) from 1 assay(s)
Binding MOAD:  1SBR Kd: 1.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 82.49β = 90
c = 86.11γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection