PDBsum entry 1q9s

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Transferase PDB id
Protein chain
149 a.a. *
Waters ×86
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of riboflavin kinase with ternary product complex
Structure: Hypothetical protein flj11149. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: flj11149. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.42Å     R-factor:   0.199     R-free:   0.260
Authors: S.Karthikeyan,Q.Zhou,A.L.Osterman,H.Zhang
Key ref:
S.Karthikeyan et al. (2003). Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism. Biochemistry, 42, 12532-12538. PubMed id: 14580199 DOI: 10.1021/bi035450t
25-Aug-03     Release date:   16-Dec-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q969G6  (RIFK_HUMAN) -  Riboflavin kinase
155 a.a.
149 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Riboflavin kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + riboflavin = ADP + FMN
+ riboflavin
Bound ligand (Het Group name = ADP)
corresponds exactly
Bound ligand (Het Group name = FMN)
corresponds exactly
      Cofactor: Mg(2+) or Zn(2+) or Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     small molecule metabolic process   10 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1021/bi035450t Biochemistry 42:12532-12538 (2003)
PubMed id: 14580199  
Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism.
S.Karthikeyan, Q.Zhou, A.L.Osterman, H.Zhang.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21371326 T.Li, H.L.Bonkovsky, and J.T.Guo (2011).
Structural analysis of heme proteins: implications for design and prediction.
  BMC Struct Biol, 11, 13.  
  19827144 M.Brylinski, and J.Skolnick (2010).
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.
  J Comput Chem, 31, 1093-1105.  
19136717 S.Frago, A.Velázquez-Campoy, and M.Medina (2009).
The Puzzle of Ligand Binding to Corynebacterium ammoniagenes FAD Synthetase.
  J Biol Chem, 284, 6610-6619.  
18713732 F.J.Sandoval, Y.Zhang, and S.Roje (2008).
  J Biol Chem, 283, 30890-30900.  
17680687 M.Brylinski, and J.Skolnick (2008).
What is the relationship between the global structures of apo and holo proteins?
  Proteins, 70, 363-377.  
18811972 S.Frago, M.Martínez-Júlvez, A.Serrano, and M.Medina (2008).
Structural analysis of FAD synthetase from Corynebacterium ammoniagenes.
  BMC Microbiol, 8, 160.  
18073108 M.Ammelburg, M.D.Hartmann, S.Djuranovic, V.Alva, K.K.Koretke, J.Martin, G.Sauer, V.Truffault, K.Zeth, A.N.Lupas, and M.Coles (2007).
A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
  Structure, 15, 1577-1590.
PDB codes: 2p3m 2vbs 2vbt 2vbu 2vbv
16183635 F.J.Sandoval, and S.Roje (2005).
An FMN hydrolase is fused to a riboflavin kinase homolog in plants.
  J Biol Chem, 280, 38337-38345.  
15771780 S.Cheek, K.Ginalski, H.Zhang, and N.V.Grishin (2005).
A comprehensive update of the sequence and structure classification of kinases.
  BMC Struct Biol, 5, 6.  
15166214 J.Li, R.M.Wynn, M.Machius, J.L.Chuang, S.Karthikeyan, D.R.Tomchick, and D.T.Chuang (2004).
Cross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase.
  J Biol Chem, 279, 32968-32978.
PDB codes: 1v11 1v16 1v1m 1v1r
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