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Protein

Riboflavin kinase

Gene

ribK

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 (PubMed:18245297) or not (PubMed:18073108).2 Publications

Catalytic activityi

CTP + riboflavin = CDP + FMN.2 Publications

Cofactori

Mg2+Note: 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.

Kineticsi

  1. KM=159 µM for riboflavin1 Publication
  2. KM=1.8 mM for CTP1 Publication
  1. Vmax=1.3 µmol/min/mg enzyme1 Publication

Pathwayi: FMN biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes FMN from riboflavin (CTP route).
Proteins known to be involved in this subpathway in this organism are:
  1. Riboflavin kinase (ribK)
This subpathway is part of the pathway FMN biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes FMN from riboflavin (CTP route), the pathway FMN biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi39Magnesium1 Publication1
Metal bindingi41Magnesium1 Publication1
Binding sitei95FMN1
Binding sitei96FMN1
Binding sitei103FMN1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15CDP1 Publication6
Nucleotide bindingi108 – 111CDP1 Publication4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

Flavoprotein, FMN, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13864.
BRENDAi2.7.1.161. 3260.
UniPathwayiUPA00276; UER00929.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin kinase (EC:2.7.1.161)
Short name:
RFK
Alternative name(s):
CTP-dependent riboflavin kinase
CTP:riboflavin 5'-phosphotransferase
Flavokinase
Gene namesi
Name:ribK
Ordered Locus Names:MJ0056
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001066731 – 132Riboflavin kinaseAdd BLAST132

Interactioni

Subunit structurei

Monomer.3 Publications

Protein-protein interaction databases

STRINGi243232.MJ_0056.

Structurei

Secondary structure

1132
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 8Combined sources8
Helixi13 – 18Combined sources6
Helixi21 – 31Combined sources11
Beta strandi40 – 48Combined sources9
Helixi50 – 52Combined sources3
Beta strandi56 – 58Combined sources3
Beta strandi61 – 63Combined sources3
Beta strandi66 – 68Combined sources3
Beta strandi71 – 80Combined sources10
Beta strandi83 – 93Combined sources11
Beta strandi99 – 105Combined sources7
Helixi110 – 113Combined sources4
Beta strandi121 – 127Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OYNX-ray1.85A1-132[»]
2P3MNMR-A1-132[»]
2VBSX-ray3.00A1-132[»]
2VBTX-ray2.70A1-132[»]
2VBUX-ray1.70A1-132[»]
2VBVX-ray2.40A/B1-132[»]
SMRiQ60365.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ60365.

Family & Domainsi

Sequence similaritiesi

Belongs to the archaeal riboflavin kinase family.Curated

Phylogenomic databases

eggNOGiarCOG01904. Archaea.
COG1339. LUCA.
InParanoidiQ60365.
KOiK07732.

Family and domain databases

Gene3Di2.40.30.30. 1 hit.
HAMAPiMF_01285. Riboflavin_kinase. 1 hit.
InterProiIPR023470. Riboflavin_kinase_archaeal.
IPR015865. Riboflavin_kinase_bac/euk.
IPR023602. Riboflavin_kinase_CTP-dep.
IPR023465. Riboflavin_kinase_domain.
[Graphical view]
PfamiPF01982. CTP-dep_RFKase. 1 hit.
[Graphical view]
SUPFAMiSSF82114. SSF82114. 1 hit.

Sequencei

Sequence statusi: Complete.

Q60365-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIIEGEVVSG LGEGRYFLSL PPYKEIFKKI LGFEPYEGTL NLKLDREFDI
60 70 80 90 100
NKFKYIETED FEFNGKRFFG VKVLPIKILI GNKKIDGAIV VPKKTYHSSE
110 120 130
IIEIIAPMKL REQFNLKDGD VIKILIKGDK DE
Length:132
Mass (Da):15,214
Last modified:April 5, 2011 - v2
Checksum:i12B9AF1567F7D8B8
GO

Sequence cautioni

The sequence AAB98036 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Mass spectrometryi

Molecular mass is 15218.1±10 Da from positions 1 - 132. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98036.1. Different initiation.
PIRiH64306.
RefSeqiWP_064496379.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98036; AAB98036; MJ_0056.
GeneIDi1450895.
KEGGimja:MJ_0056.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98036.1. Different initiation.
PIRiH64306.
RefSeqiWP_064496379.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OYNX-ray1.85A1-132[»]
2P3MNMR-A1-132[»]
2VBSX-ray3.00A1-132[»]
2VBTX-ray2.70A1-132[»]
2VBUX-ray1.70A1-132[»]
2VBVX-ray2.40A/B1-132[»]
SMRiQ60365.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0056.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98036; AAB98036; MJ_0056.
GeneIDi1450895.
KEGGimja:MJ_0056.

Phylogenomic databases

eggNOGiarCOG01904. Archaea.
COG1339. LUCA.
InParanoidiQ60365.
KOiK07732.

Enzyme and pathway databases

UniPathwayiUPA00276; UER00929.
BioCyciMetaCyc:MONOMER-13864.
BRENDAi2.7.1.161. 3260.

Miscellaneous databases

EvolutionaryTraceiQ60365.

Family and domain databases

Gene3Di2.40.30.30. 1 hit.
HAMAPiMF_01285. Riboflavin_kinase. 1 hit.
InterProiIPR023470. Riboflavin_kinase_archaeal.
IPR015865. Riboflavin_kinase_bac/euk.
IPR023602. Riboflavin_kinase_CTP-dep.
IPR023465. Riboflavin_kinase_domain.
[Graphical view]
PfamiPF01982. CTP-dep_RFKase. 1 hit.
[Graphical view]
SUPFAMiSSF82114. SSF82114. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRIFK_METJA
AccessioniPrimary (citable) accession number: Q60365
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: April 5, 2011
Last modified: November 2, 2016
This is version 86 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.