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Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.1 Publication

Catalytic activityi

1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate.1 Publication

Kineticsi

  1. KM=4.2 µM for 5-amino-6-(D-ribitylamino)uracil1 Publication
  2. KM=62 µM for 3,4-dihydroxy-2-butanone 4-phosphate1 Publication
  1. Vmax=11800 nmol/h/mg enzyme1 Publication

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil.1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. 6,7-dimethyl-8-ribityllumazine synthase (ribE)
  2. Riboflavin synthase (ribC)
This subpathway is part of the pathway riboflavin 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 riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei225-amino-6-(D-ribitylamino)uracilBy similarity1
Active sitei89Proton donorSequence analysis1
Binding sitei1145-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei1281-deoxy-L-glycero-tetrulose 4-phosphateBy similarity1

GO - Molecular functioni

  • 6,7-dimethyl-8-ribityllumazine synthase activity Source: EcoCyc
  • transferase activity Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:LUMAZINESYN-MONOMER.
ECOL316407:JW0405-MONOMER.
MetaCyc:LUMAZINESYN-MONOMER.
SABIO-RKP61714.
UniPathwayiUPA00275; UER00404.

Names & Taxonomyi

Protein namesi
Recommended name:
6,7-dimethyl-8-ribityllumazine synthase (EC:2.5.1.78)
Short name:
DMRL synthase
Short name:
LS
Short name:
Lumazine synthase
Gene namesi
Name:ribE
Synonyms:ribH, ybaF
Ordered Locus Names:b0415, JW0405
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11322. ribE.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • riboflavin synthase complex Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001347541 – 1566,7-dimethyl-8-ribityllumazine synthaseAdd BLAST156

Proteomic databases

EPDiP61714.
PaxDbiP61714.
PRIDEiP61714.

2D gel databases

SWISS-2DPAGEP61714.

Interactioni

Subunit structurei

Forms a hollow icosahedral capsid composed of 60 subunits, probably arranged as a dodecamer of pentamers. Unlike in B.subtilis, does not interact with riboflavin synthase, and the core of the icosahedral capsid is empty.1 Publication

Protein-protein interaction databases

BioGridi4259505. 63 interactors.
DIPiDIP-10711N.
IntActiP61714. 15 interactors.
MINTiMINT-1225919.
STRINGi511145.b0415.

Structurei

3D structure databases

ProteinModelPortaliP61714.
SMRiP61714.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni57 – 595-amino-6-(D-ribitylamino)uracil bindingBy similarity3
Regioni81 – 835-amino-6-(D-ribitylamino)uracil bindingBy similarity3
Regioni86 – 871-deoxy-L-glycero-tetrulose 4-phosphate bindingBy similarity2

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229250.
InParanoidiP61714.
KOiK00794.
OMAiSHVAMNS.
PhylomeDBiP61714.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth. 1 hit.
InterProiIPR002180. DMRL_synthase.
[Graphical view]
PANTHERiPTHR21058. PTHR21058. 1 hit.
PfamiPF00885. DMRL_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF52121. SSF52121. 1 hit.
TIGRFAMsiTIGR00114. lumazine-synth. 1 hit.

Sequencei

Sequence statusi: Complete.

P61714-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIIEANVAT PDARVAITIA RFNNFINDSL LEGAIDALKR IGQVKDENIT
60 70 80 90 100
VVWVPGAYEL PLAAGALAKT GKYDAVIALG TVIRGGTAHF EYVAGGASNG
110 120 130 140 150
LAHVAQDSEI PVAFGVLTTE SIEQAIERAG TKAGNKGAEA ALTALEMINV

LKAIKA
Length:156
Mass (Da):16,157
Last modified:June 7, 2004 - v1
Checksum:i1F8504B2892195C7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X64395 Genomic DNA. Translation: CAA45736.1.
U82664 Genomic DNA. Translation: AAB40171.1.
U00096 Genomic DNA. Translation: AAC73518.1.
AP009048 Genomic DNA. Translation: BAE76195.1.
PIRiS26202.
RefSeqiNP_414949.1. NC_000913.3.
WP_001021161.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73518; AAC73518; b0415.
BAE76195; BAE76195; BAE76195.
GeneIDi946453.
KEGGiecj:JW0405.
eco:b0415.
PATRICi32115979. VBIEscCol129921_0431.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X64395 Genomic DNA. Translation: CAA45736.1.
U82664 Genomic DNA. Translation: AAB40171.1.
U00096 Genomic DNA. Translation: AAC73518.1.
AP009048 Genomic DNA. Translation: BAE76195.1.
PIRiS26202.
RefSeqiNP_414949.1. NC_000913.3.
WP_001021161.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP61714.
SMRiP61714.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259505. 63 interactors.
DIPiDIP-10711N.
IntActiP61714. 15 interactors.
MINTiMINT-1225919.
STRINGi511145.b0415.

2D gel databases

SWISS-2DPAGEP61714.

Proteomic databases

EPDiP61714.
PaxDbiP61714.
PRIDEiP61714.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73518; AAC73518; b0415.
BAE76195; BAE76195; BAE76195.
GeneIDi946453.
KEGGiecj:JW0405.
eco:b0415.
PATRICi32115979. VBIEscCol129921_0431.

Organism-specific databases

EchoBASEiEB1298.
EcoGeneiEG11322. ribE.

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229250.
InParanoidiP61714.
KOiK00794.
OMAiSHVAMNS.
PhylomeDBiP61714.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BioCyciEcoCyc:LUMAZINESYN-MONOMER.
ECOL316407:JW0405-MONOMER.
MetaCyc:LUMAZINESYN-MONOMER.
SABIO-RKP61714.

Miscellaneous databases

PROiP61714.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth. 1 hit.
InterProiIPR002180. DMRL_synthase.
[Graphical view]
PANTHERiPTHR21058. PTHR21058. 1 hit.
PfamiPF00885. DMRL_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF52121. SSF52121. 1 hit.
TIGRFAMsiTIGR00114. lumazine-synth. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRISB_ECOLI
AccessioniPrimary (citable) accession number: P61714
Secondary accession number(s): P25540, P77114, Q2MC11
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: June 7, 2004
Last modified: November 2, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.