Q60365 (RIFK_METJA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Riboflavin kinase
Short name=RFK
EC=2.7.1.161

Alternative name(s):
CTP-dependent riboflavin kinase
CTP:riboflavin 5'-phosphotransferase
Flavokinase

Gene names

Name:	ribK
Ordered Locus Names:	MJ0056

Organism

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)

Taxonomic identifier

243232 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

Protein attributes

Sequence length	132 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the CTP-dependent phosphorylation of riboflavin (vitamin B2) to form flavin mononucleotide (FMN). Can also utilize UTP as the phosphate donor, although less efficiently, and it is unclear if ATP and GTP can also serve as substrates (Ref.2) or not (Ref.4). Ref.2 Ref.4
Catalytic activity	CTP + riboflavin = CDP + FMN. Ref.2 Ref.4
Cofactor	Binds 1 magnesium ion per subunit. This ion is coordinated by a threonine and an asparagine, and by the alpha- and beta-phosphates of CDP.
Pathway	Cofactor biosynthesis; FMN biosynthesis; FMN from riboflavin (CTP route): step 1/1. HAMAP MF_01285
Subunit structure	Monomer. Ref.2 Ref.4
Sequence similarities	Belongs to the archaeal riboflavin kinase family.
Biophysicochemical properties	Kinetic parameters: KM=159 µM for riboflavin Ref.2 KM=1.8 mM for CTP Vmax=1.3 µmol/min/mg enzyme
Mass spectrometry	Molecular mass is 15218.1±10 Da from positions 1 - 132. Determined by ESI. Ref.2
Sequence caution	The sequence AAB98036.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Ligand	FMN Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	riboflavin biosynthetic process Inferred from electronic annotation. Source: InterPro
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW riboflavin kinase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 132

132

Riboflavin kinase HAMAP MF_01285

PRO_0000106673

Regions

Nucleotide binding

10 – 15

6

CDP HAMAP MF_01285

Nucleotide binding

108 – 111

4

CDP HAMAP MF_01285

Sites

Metal binding

39

1

Magnesium

Metal binding

41

1

Magnesium

Binding site

95

1

FMN

Binding site

96

1

FMN

Binding site

103

1

FMN

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

132

Helix Strand Turn

Details...

Beta strand

1 – 8

8

Helix

13 – 17

5

Helix

21 – 31

11

Beta strand

40 – 48

9

Helix

50 – 52

3

Beta strand

61 – 63

3

Beta strand

66 – 68

3

Beta strand

71 – 80

10

Beta strand

83 – 94

12

Beta strand

99 – 105

7

Helix

110 – 114

5

Beta strand

121 – 127

7

Sequences

	Sequence		Length	Mass (Da)
	Q60365 [UniParc]. Last modified April 5, 2011. Version 2. Checksum: 12B9AF1567F7D8B8	FASTA	132	15,214
	10 20 30 40 50 60 MIIEGEVVSG LGEGRYFLSL PPYKEIFKKI LGFEPYEGTL NLKLDREFDI NKFKYIETED 70 80 90 100 110 120 FEFNGKRFFG VKVLPIKILI GNKKIDGAIV VPKKTYHSSE IIEIIAPMKL REQFNLKDGD 130 VIKILIKGDK DE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Identification and characterization of an archaeon-specific riboflavin kinase." Mashhadi Z., Zhang H., Xu H., White R.H. J. Bacteriol. 190:2615-2618(2008) [PubMed: 18245297] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY, GENE NAME, MASS SPECTROMETRY, SUBUNIT.
[3]	"Crystal structure of hypothetical protein from Methanococcus jannaschii bound to CDP." New York structural genomics research consortium (NYSGRC) Submitted (MAR-2007) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH CDP.
[4]	"A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels." Ammelburg M., Hartmann M.D., Djuranovic S., Alva V., Koretke K.K., Martin J., Sauer G., Truffault V., Zeth K., Lupas A.N., Coles M. Structure 15:1577-1590(2007) [PubMed: 18073108] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH REACTION PRODUCTS AND MAGNESIUM, STRUCTURE BY NMR, FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION, SUBSTRATE SPECIFICITY, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L77117 Genomic DNA. Translation: AAB98036.1. Different initiation.

PIR

H64306.

RefSeq

NP_247020.1. NC_000909.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2OYN	X-ray	1.85	A	1-132	[»]
2P3M	NMR	-	A	1-132	[»]
2VBS	X-ray	3.00	A	1-132	[»]
2VBT	X-ray	2.70	A	1-132	[»]
2VBU	X-ray	1.70	A	1-132	[»]
2VBV	X-ray	2.40	A/B	1-132	[»]

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1450895.

GenomeReviews

Gene locus MJ0056 in contig L77117_GR.

KEGG

mja:MJ_0056.

NMPDR

fig|243232.1.peg.57.

TIGR

MJ0056.

Phylogenomic databases

HOGENOM

HBG553349.

ProtClustDB

PRK14132.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-13864.
MJAN243232:MJ_0056-MONOMER.

BRENDA

2.7.1.161. 3260.

Family and domain databases

HAMAP

MF_01285. Riboflavin_kinase.
[Tree]

InterPro

IPR023470. Riboflavin_kinase_archaeal.
IPR023602. Riboflavin_kinase_CTP-dep.
IPR023465. Riboflavin_kinase_domain.
[Graphical view]

Gene3D

G3DSA:2.40.30.30. Riboflavin_kinase. 1 hit.

KO

K07732.

Pfam

PF01982. CTP-dep_RFKase. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RIFK_METJA

Accession

Primary (citable) accession number: Q60365

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	April 5, 2011
Last modified:	November 16, 2011
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program