Crystal structure of riboflavin kinase with ternary product complex

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism.

Karthikeyan, S.Zhou, Q.Osterman, A.L.Zhang, H.

(2003) Biochemistry 42: 12532-12538

  • DOI: https://doi.org/10.1021/bi035450t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Riboflavin kinase (RFK) is an essential enzyme catalyzing the phosphorylation of riboflavin (vitamin B(2)) in the presence of ATP and Mg(2+) to form the active cofactor FMN, which can be further converted to FAD. Previously, the crystal structures of RFKs from human and Schizosaccharomyces pombe have been determined in the apo form and in complex with MgADP. These structures revealed that RFK adopts a novel kinase fold and utilizes a unique nucleotide binding site. The structures of the flavin-bound RFK obtained by soaking pre-existing crystals were also reported. Because of crystal packing restraints, these flavin-bound RFK complexes adopt conformations nearly identical with that of corresponding flavin-free structures. Here we report the structure of human RFK cocrystallized with both MgADP and FMN. Drastic conformational changes associated with flavin binding are observed primarily at the so-called Flap I and Flap II loop regions. As a result, the bound FMN molecule now interacts with the enzyme extensively and is well-ordered. Residues from Flap II interact with Flap I and shield the FMN molecule from the solvent. The conformational changes in Flap I resulted in a new Mg(2+) coordination pattern in which a FMN phosphate oxygen and Asn36 side chain carbonyl are directly coordinating to the Mg(2+) ion. The proposed catalytic base Glu86 is well-positioned for activation of the O5' hydroxyl group of riboflavin for the phosphoryl transfer reaction. The structural data obtained so far on human and yeast RFK complexes provide a rationale for the ordered kinetic mechanism of RFK.

  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein FLJ11149149Homo sapiensMutation(s): 0 
Gene Names: FLJ11149
UniProt & NIH Common Fund Data Resources
Find proteins for Q969G6 (Homo sapiens)
Explore Q969G6 
Go to UniProtKB:  Q969G6
GTEx:  ENSG00000135002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969G6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.312α = 90
b = 118.789β = 90
c = 37.979γ = 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: 2003-12-16
    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: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description