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30  structures 4531  species 2  interactions 4738  sequences 21  architectures

Family: Flavokinase (PF01687)

Summary: Riboflavin kinase

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This is the Wikipedia entry entitled "Riboflavin kinase". More...

Riboflavin kinase Edit Wikipedia article

riboflavin kinase
Riboflavkinase.png
Crystal structure of riboflavin kinase from Thermoplasma acidophilum.[1]
Identifiers
EC number 2.7.1.26
CAS number 9032-82-0
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Riboflavin kinase
PDB 1s4m EBI.jpg
crystal structure of flavin binding to fad synthetase from thermotoga maritina
Identifiers
Symbol Flavokinase
Pfam PF01687
InterPro IPR015865
SCOP 1mrz
SUPERFAMILY 1mrz
Riboflavin kinase
Identifiers
Symbol Riboflavin_kinase
Pfam PF01687
InterPro IPR015865

In enzymology, a riboflavin kinase (EC 2.7.1.26) is an enzyme that catalyzes the chemical reaction

ATP + riboflavin \rightleftharpoons ADP + FMN

Thus, the two substrates of this enzyme are ATP and riboflavin, whereas its two products are ADP and FMN.

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (EC 2.7.1.26), which converts it into FMN, and FAD synthetase (EC 2.7.7.2), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme,[2] the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family.[3] The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases.[4]

This enzyme belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:riboflavin 5'-phosphotransferase. This enzyme is also called flavokinase. This enzyme participates in riboflavin metabolism.

However, archaeal riboflavin kinases (EC 2.7.1.161) are, in general, utilizing CTP rather than ATP as the donor nucleotide, catalyzing the reaction

CTP + riboflavin \rightleftharpoons CDP + FMN [5]

Riboflavin kinase can also be isolated from other types of bacteria, all with similar function but a different number of amino acids.

Structure[edit]

A hydropathy plot for Riboflavin Kinase.
A hydropathy plot for Riboflavin Kinase.

The complete enzyme arrangement can be observed with X-ray crystallography and with NMR. The riboflavin kinase enzyme isolated from Thermoplasma acidophilum contains 220 amino acids. The structure of this enzyme has been determined X-ray crystallography at a resolution of 2.20 Å. Its secondary structure contains 69 residues (30%) in alpha helix form, and 60 residues (26%) a beta sheet conformation. The enzyme contains a magnesium binding site at amino acids 131 and 133, and a Flavin mononucleotide binding site at amino acids 188 and 195.

As of late 2007, 14 structures have been solved for this class of enzymes, with PDB accession codes 1N05, 1N06, 1N07, 1N08, 1NB0, 1NB9, 1P4M, 1Q9S, 2P3M, 2VBS, 2VBT, 3CTA, 2VBU, and 2VBV.

References[edit]

  1. ^ PDB 3CTA; Bonanno, J.B., Rutter, M., Bain, K.T., Mendoza, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C. (2008). Crystal structure of riboflavin kinase from Thermoplasma acidophilum. 
  2. ^ Osterman AL, Zhang H, Zhou Q, Karthikeyan S (2003). "Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism". Biochemistry 42 (43): 12532–8. doi:10.1021/bi035450t. PMID 14580199. 
  3. ^ Galluccio M, Brizio C, Torchetti EM, Ferranti P, Gianazza E, Indiveri C, Barile M (2007). "Over-expression in Escherichia coli, purification and characterization of isoform 2 of human FAD synthetase". Protein Expr. Purif. 52 (1): 175–81. doi:10.1016/j.pep.2006.09.002. PMID 17049878. 
  4. ^ Srinivasan N, Krupa A, Sandhya K, Jonnalagadda S (2003). "A conserved domain in prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer". Trends Biochem. Sci. 28 (1): 9–12. doi:10.1016/S0968-0004(02)00009-9. PMID 12517446. 
  5. ^ Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M (2007). "A CTP-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels". Structure. 12 (12): 1577–90. doi:10.1016/j.str.2007.09.027. PMID 18073108. 

Further reading[edit]

  • CHASSY BM, ARSENIS C, MCCORMICK DB (1965). "THE EFFECT OF THE LENGTH OF THE SIDE CHAIN OF FLAVINS ON REACTIVITY WITH FLAVOKINASE". J. Biol. Chem. 240: 1338–40. PMID 14284745. 
  • GIRI KV, KRISHNASWAMY PR, RAO NA (1958). "Studies on plant flavokinase". Biochem. J. 70 (1): 66–71. PMC 1196627. PMID 13584303. 
  • KEARNEY EB (1952). "The interaction of yeast flavokinase with riboflavin analogues". J. Biol. Chem. 194 (2): 747–54. PMID 14927668. 
  • McCormick DB and Butler RC (1962). "Substrate specificity of liver flavokinase". Biochim. Biophys. Acta 65 (2): 326–332. doi:10.1016/0006-3002(62)91051-X. 
  • Sandoval FJ, Roje S (2005). "An FMN hydrolase is fused to a riboflavin kinase homolog in plants". J. Biol. Chem. 280 (46): 38337–45. doi:10.1074/jbc.M500350200. PMID 16183635. 
  • Solovieva IM, Tarasov KV, Perumov DA (Mosc). "Main physicochemical features of monofunctional flavokinase from Bacillus subtilis". B. Biochemistry. (2): 177–81. PMID 12693963. 
  • Solovieva IM, Kreneva RA, Leak DJ, Perumov DA (Pt 1). "The ribR gene encodes a monofunctional riboflavin kinase which is involved in regulation of the Bacillus subtilis riboflavin operon". Microbiology. 145: 67–73. doi:10.1099/13500872-145-1-67. PMID 10206712. 

This article incorporates text from the public domain Pfam and InterPro IPR015865

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Riboflavin kinase Provide feedback

This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism [1]. This domain is thought to have kinase activity [2].

Literature references

  1. Mack M, van Loon AP, Hohmann HP; , J Bacteriol 1998;180:950-955.: Regulation of riboflavin biosynthesis in Bacillus subtilis is affected by the activity of the flavokinase/flavin adenine dinucleotide synthetase encoded by ribC. PUBMED:9473052 EPMC:9473052

  2. Wang W, Kim R, Yokota H, Kim SH; , Proteins 2005;58:246-248.: Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima. PUBMED:15468322 EPMC:15468322


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015865

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (EC), which converts it into FMN, and FAD synthetase (EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [PUBMED:14580199], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family [PUBMED:17049878]. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases [PUBMED:12517446].

This entry represents the riboflavin kinase domains from bacteria and eukaryotes.

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Domain organisation

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Full
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Representative proteomes NCBI
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Meta
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RP15
(411)
RP35
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RP55
(1021)
RP75
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  Seed
(139)
Full
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Representative proteomes NCBI
(3417)
Meta
(2167)
RP15
(411)
RP35
(772)
RP55
(1021)
RP75
(1203)
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Curation and family details

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Seed source: Pfam-B_1221 (release 4.1)
Previous IDs: FAD_Synth;
Type: Domain
Author: Bashton M, Bateman A, Mistry J, Eddy S
Number in seed: 139
Number in full: 4738
Average length of the domain: 126.90 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 41.33 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.6 19.6
Trusted cut-off 20.6 20.5
Noise cut-off 18.7 18.2
Model length: 125
Family (HMM) version: 12
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Interactions

There are 2 interactions for this family. More...

FAD_syn Flavokinase

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Flavokinase domain has been found. There are 30 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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