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PDBsum entry 1n06

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1n06
Jmol
Contents
Protein chains
154 a.a. *
Ligands
ADP ×2
Waters ×155
* Residue conservation analysis
PDB id:
1n06
Name: Transferase
Title: Crystal structure of schizosaccharomyces pombe riboflavin kinase reveals a novel atp and riboflavin binding fold
Structure: Putative riboflavin kinase. Chain: a, b. Engineered: yes
Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: spcc18.16.C. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.238     R-free:   0.274
Authors: S.Bauer,K.Kemter,A.Bacher,R.Huber,M.Fischer,S.Steinbacher
Key ref:
S.Bauer et al. (2003). Crystal structure of Schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin-binding fold. J Mol Biol, 326, 1463-1473. PubMed id: 12595258 DOI: 10.1016/S0022-2836(03)00059-7
Date:
11-Oct-02     Release date:   25-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O74866  (RIFK_SCHPO) -  Riboflavin kinase
Seq:
Struc:
163 a.a.
154 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.26  - Riboflavin kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + riboflavin = ADP + FMN
ATP
+ riboflavin
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ FMN
      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     nucleus   3 terms 
  Biological process     phosphorylation   4 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(03)00059-7 J Mol Biol 326:1463-1473 (2003)
PubMed id: 12595258  
 
 
Crystal structure of Schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin-binding fold.
S.Bauer, K.Kemter, A.Bacher, R.Huber, M.Fischer, S.Steinbacher.
 
  ABSTRACT  
 
The essential redox cofactors riboflavin monophosphate (FMN) and flavin adenine dinucleotide (FAD) are synthesised from their precursor, riboflavin, in sequential reactions by the metal-dependent riboflavin kinase and FAD synthetase. Here, we describe the 1.6A crystal structure of the Schizosaccharomyces pombe riboflavin kinase. The enzyme represents a novel family of phosphoryl transferring enzymes. It is a monomer comprising a central beta-barrel clasped on one side by two C-terminal helices that display an L-like shape. The opposite side of the beta-barrel serves as a platform for substrate binding as demonstrated by complexes with ADP and FMN. Formation of the ATP-binding site requires significant rearrangements in a short alpha-helix as compared to the substrate free form. The diphosphate moiety of ADP is covered by the glycine-rich flap I formed from parts of this alpha-helix. In contrast, no significant changes are observed upon binding of riboflavin. The ribityl side-chain might be covered by a rather flexible flap II. The unusual metal-binding site involves, in addition to the ADP phosphates, only the strictly conserved Thr45. This may explain the preference for zinc observed in vitro.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Reaction catalysed by riboflavin kinase and FAD synthetase. 1, Riboflavin; 2, FMN; 3, FAD.
Figure 5.
Figure 5. Proposed catalytic mechanism of riboflavin synthase. (a) Stereo drawings of the active site of the riboflavin kinase. Bound FMN and ADP are shown as ball-and-stick models. The position of the zinc ion was taken from ADP+Zn complex. Flap I covers the b and g phosphate-binding sites. (b) Residues involved in catalysis.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 1463-1473) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20955574 I.Yruela, S.Arilla-Luna, M.Medina, and B.Contreras-Moreira (2010).
Evolutionary divergence of chloroplast FAD synthetase proteins.
  BMC Evol Biol, 10, 311.  
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.  
19049514 T.A.Giancaspero, V.Locato, M.C.de Pinto, L.De Gara, and M.Barile (2009).
The occurrence of riboflavin kinase and FAD synthetase ensures FAD synthesis in tobacco mitochondria and maintenance of cellular redox status.
  FEBS J, 276, 219-231.  
18713732 F.J.Sandoval, Y.Zhang, and S.Roje (2008).
Flavin Nucleotide Metabolism in Plants: MONOFUNCTIONAL ENZYMES SYNTHESIZE FAD IN PLASTIDS.
  J Biol Chem, 283, 30890-30900.  
18811972 S.Frago, M.Martínez-Júlvez, A.Serrano, and M.Medina (2008).
Structural analysis of FAD synthetase from Corynebacterium ammoniagenes.
  BMC Microbiol, 8, 160.  
18245297 Z.Mashhadi, H.Zhang, H.Xu, and R.H.White (2008).
Identification and characterization of an archaeon-specific riboflavin kinase.
  J Bacteriol, 190, 2615-2618.  
17154432 A.K.Hirsch, F.R.Fischer, and F.Diederich (2007).
Phosphate recognition in structural biology.
  Angew Chem Int Ed Engl, 46, 338-352.  
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
17944933 W.Eisenreich, M.Joshi, B.Illarionov, G.Richter, W.Römisch-Margl, F.Müller, A.Bacher, and M.Fischer (2007).
13C Isotopologue editing of FMN bound to phototropin domains.
  FEBS J, 274, 5876-5890.  
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.  
16010344 M.Fischer, and A.Bacher (2005).
Biosynthesis of flavocoenzymes.
  Nat Prod Rep, 22, 324-350.  
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.  
15468322 W.Wang, R.Kim, H.Yokota, and S.H.Kim (2005).
Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima.
  Proteins, 58, 246-248.
PDB code: 1s4m
15598351 S.Cheek, Y.Qi, S.S.Krishna, L.N.Kinch, and N.V.Grishin (2004).
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
  BMC Bioinformatics, 5, 197.  
14580199 S.Karthikeyan, Q.Zhou, A.L.Osterman, and H.Zhang (2003).
Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism.
  Biochemistry, 42, 12532-12538.
PDB code: 1q9s
12904291 S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, and M.Fischer (2003).
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.
  J Biol Chem, 278, 42256-42265.
PDB codes: 1pvw 1pvy
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.