Summary: Riboflavin kinase

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Wikipedia: Riboflavin kinase
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Riboflavin kinase Edit Wikipedia article

riboflavin kinase

Crystal structure of riboflavin kinase from Thermoplasma acidophilum.^[1]

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Riboflavin kinase

crystal structure of flavin binding to fad synthetase from thermotoga maritina

Identifiers

Symbol

Flavokinase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Riboflavin kinase

Identifiers

Symbol

Riboflavin_kinase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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.

[edit] Structure

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.

[edit] References

^ 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.
^ 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.
^ 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.
^ 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.
^ 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. http://www.uniprot.org/uniprot/Q9HJA6.

[edit] Further reading

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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1196627/.
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.

Metabolism of vitamins, coenzymes, and cofactors

Fat soluble vitamins

Vitamin A	Retinol binding protein

Vitamin E	Alpha-tocopherol transfer protein

Vitamin D	liver (Sterol 27-hydroxylase or CYP27A1) · renal (25-Hydroxyvitamin D₃ 1-alpha-hydroxylase or CYP27B1) · degradation (1,25-Dihydroxyvitamin D₃ 24-hydroxylase or CYP24A1)

Vitamin K	Vitamin K epoxide reductase

Water soluble vitamins

Thiamine (B₁)	Thiamine diphosphokinase

Niacin (B₃)	Indoleamine 2,3-dioxygenase · Formamidase

Pantothenic acid (B₅)	Pantothenate kinase

Folic acid (B₉)	Dihydropteroate synthase · Dihydrofolate reductase · Serine hydroxymethyltransferase Methylenetetrahydrofolate reductase

Vitamin B₁₂	MMAA · MMAB · MMACHC · MMADHC

Vitamin C	L-gulonolactone oxidase

Riboflavin (B₂)	Riboflavin kinase

Nonvitamin cofactors

Tetrahydrobiopterin	GTP cyclohydrolase I · 6-pyruvoyltetrahydropterin synthase · Sepiapterin reductase PCBD1 · PTS · QDPR

Molybdenum cofactor	MOCS1 · MOCS2 · MOCS3 · GPHN

M: NUT

cof, enz, met

noco, nuvi, sysi/epon, met

drug (A8/11/12)

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

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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

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
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

PANDIT:	PF01687
Pseudofam:	PF01687
SCOP:	1mrz
SYSTERS:	Flavokinase

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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	riboflavin kinase activity (GO:0008531)
Biological process	riboflavin biosynthetic process (GO:0009231)

Domain organisation

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Alignments

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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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	Seed (139)	Full (4738)	Representative proteomes				NCBI (3417)	Meta (2167)
	Seed (139)	Full (4738)	RP15 (411)	RP35 (772)	RP55 (1021)	RP75 (1203)	NCBI (3417)	Meta (2167)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (139)	Full (4738)	Representative proteomes				NCBI (3417)	Meta (2167)
	Seed (139)	Full (4738)	RP15 (411)	RP35 (772)	RP55 (1021)	RP75 (1203)	NCBI (3417)	Meta (2167)
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	Seed (139)	Full (4738)	Representative proteomes				NCBI (3417)	Meta (2167)
	Seed (139)	Full (4738)	RP15 (411)	RP35 (772)	RP55 (1021)	RP75 (1203)	NCBI (3417)	Meta (2167)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

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 %

HMM information

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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Species distribution

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Interactive tree

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Interactions

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

Flavokinase FAD_syn

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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Flavokinase (PF01687)

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Summary: Riboflavin kinase

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Riboflavin kinase Edit Wikipedia article

[edit] Structure

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[edit] Further reading

Riboflavin kinase Provide feedback

Literature references

External database links

InterPro entry IPR015865

Gene Ontology

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