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PDBsum entry 1nbg

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protein ligands metals links
Transferase PDB id
1nbg
Jmol
Contents
Protein chain
147 a.a.
Ligands
ADP
FMN
Metals
_MG
Waters ×108
Superseded by: 1p4m 1p4m
PDB id:
1nbg
Name: Transferase
Title: Crystal structure of riboflavin kinase
Structure: Hypothetical protein flj11149. Chain: a. Synonym: riboflavin kinase. Engineered: yes
Source: Homo sapiens. Human. Gene: flj11149. Expressed in: escherichia coli.
Resolution:
1.80Å     R-factor:   0.188     R-free:   0.227
Authors: S.Karthikeyan,Q.Zhou,F.Mseeh,N.V.Grishin,A.L.Osterman, H.Zhang
Key ref:
S.Karthikeyan et al. (2003). Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch. Structure, 11, 265-273. PubMed id: 12623014 DOI: 10.1016/S0969-2126(03)00024-8
Date:
02-Dec-02     Release date:   11-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 147 a.a.
Key:    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
Bound ligand (Het Group name = ADP)
matches with 87.00% similarity
+
riboflavin
Bound ligand (Het Group name = FMN)
matches with 81.00% similarity
= ADP
+ FMN
      Cofactor: Mg(2+) or Zn(2+) or Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(03)00024-8 Structure 11:265-273 (2003)
PubMed id: 12623014  
 
 
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch.
S.Karthikeyan, Q.Zhou, F.Mseeh, N.V.Grishin, A.L.Osterman, H.Zhang.
 
  ABSTRACT  
 
Riboflavin kinase (RFK) is an essential enzyme catalyzing the phosphorylation of riboflavin (vitamin B(2)) to form FMN, an obligatory step in vitamin B(2) utilization and flavin cofactor synthesis. The structure of human RFK revealed a six-stranded antiparallel beta barrel core structurally similar to the riboflavin synthase/ferredoxin reductase FAD binding domain fold. The binding site of an intrinsically bound MgADP defines a novel nucleotide binding motif that encompasses a loop, a 3(10) helix, and a reverse turn followed by a short beta strand. This active site loop forms an arch with ATP and riboflavin binding at the opposite side and the phosphoryl transfer appears to occur through the hole underneath the arch. The invariant residues Asn36 and Glu86 are implicated in the catalysis.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Fold Comparison of Riboflavin Kinase with Two Other b Barrel Flavin Binding FoldsThe last two helices (helices C and D) in hsRFK are omitted for clarity. The bound ligand(s) in each structure is shown in the ball-and-stick representation. The N and C termini and each b strand are labeled. b strands in ferric reductase are labeled in a circular permutated fashion according to the topology of phthalate dioxygenase reductase N-terminal domain.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 265-273) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21338251 M.Szczuko, T.Seidler, M.Mierzwa, E.Stachowska, and D.Chlubek (2011).
Effect of riboflavin supply on student body's provision in north-western Poland with riboflavin measured by activity of glutathione reductase considering daily intake of other nutrients.
  Int J Food Sci Nutr, 62, 431-438.  
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.  
20813848 S.J.Eussen, S.E.Vollset, S.Hustad, ..Midttun, K.Meyer, A.Fredriksen, P.M.Ueland, M.Jenab, N.Slimani, P.Boffetta, K.Overvad, O.Thorlacius-Ussing, A.Tjønneland, A.Olsen, F.Clavel-Chapelon, M.C.Boutron-Ruault, S.Morois, C.Weikert, T.Pischon, J.Linseisen, R.Kaaks, A.Trichopoulou, D.Zilis, M.Katsoulis, D.Palli, V.Pala, P.Vineis, R.Tumino, S.Panico, P.H.Peeters, H.B.Bueno-de-Mesquita, F.J.van Duijnhoven, G.Skeie, X.Muñoz, C.Martínez, M.Dorronsoro, E.Ardanaz, C.Navarro, L.Rodríguez, B.VanGuelpen, R.Palmqvist, J.Manjer, U.Ericson, S.Bingham, K.T.Khaw, T.Norat, and E.Riboli (2010).
Plasma vitamins B2, B6, and B12, and related genetic variants as predictors of colorectal cancer risk.
  Cancer Epidemiol Biomarkers Prev, 19, 2549-2561.  
19641494 B.Yazdanpanah, K.Wiegmann, V.Tchikov, O.Krut, C.Pongratz, M.Schramm, A.Kleinridders, T.Wunderlich, H.Kashkar, O.Utermöhlen, J.C.Brüning, S.Schütze, and M.Krönke (2009).
Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.
  Nature, 460, 1159-1163.  
19375431 C.Huerta, D.Borek, M.Machius, N.V.Grishin, and H.Zhang (2009).
Structure and mechanism of a eukaryotic FMN adenylyltransferase.
  J Mol Biol, 389, 388-400.
PDB codes: 3fwk 3g59 3g5a 3g6k
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.  
19558965 V.Y.Yatsyshyn, O.P.Ishchuk, A.Y.Voronovsky, D.V.Fedorovych, and A.A.Sibirny (2009).
Production of flavin mononucleotide by metabolically engineered yeast Candida famata.
  Metab Eng, 11, 163-167.  
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
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.  
14622288 M.H.Hefti, J.Vervoort, and W.J.van Berkel (2003).
Deflavination and reconstitution of flavoproteins.
  Eur J Biochem, 270, 4227-4242.  
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
12623010 Y.Lindqvist (2003).
A new kinase fold.
  Structure, 11, 241-242.  
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.