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Protein

6,7-dimethyl-8-ribityllumazine synthase 1

Gene

ribH1

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

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.UniRule annotation

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.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. 6,7-dimethyl-8-ribityllumazine synthase 2 (ribH2), 6,7-dimethyl-8-ribityllumazine synthase 1 (ribH1)
  2. no protein annotated in this organism
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei27 – 2715-amino-6-(D-ribitylamino)uracilUniRule annotation
Active sitei95 – 951Proton donorUniRule annotation
Binding sitei120 – 12015-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygenUniRule annotation
Binding sitei134 – 13411-deoxy-L-glycero-tetrulose 4-phosphateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-5066-MONOMER.
UniPathwayiUPA00275; UER00404.

Names & Taxonomyi

Protein namesi
Recommended name:
6,7-dimethyl-8-ribityllumazine synthase 1UniRule annotation (EC:2.5.1.78UniRule annotation)
Short name:
DMRL synthase 1UniRule annotation
Short name:
LS 1UniRule annotation
Short name:
Lumazine synthase 1UniRule annotation
Gene namesi
Name:ribH1UniRule annotation
Ordered Locus Names:bll5029
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
Proteomesi
  • UP000002526 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1631636,7-dimethyl-8-ribityllumazine synthase 1PRO_0000134722Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224911.bll5029.

Structurei

3D structure databases

ProteinModelPortaliQ89K80.
SMRiQ89K80. Positions 21-161.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni58 – 6035-amino-6-(D-ribitylamino)uracil bindingUniRule annotation
Regioni87 – 8935-amino-6-(D-ribitylamino)uracil bindingUniRule annotation
Regioni92 – 9321-deoxy-L-glycero-tetrulose 4-phosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the DMRL synthase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229250.
InParanoidiQ89K80.
KOiK00794.
OMAiTVCNDSS.
OrthoDBiPOG091H021R.
PhylomeDBiQ89K80.

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.

Q89K80-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADARRAPLK DQTDISGARA LIVEARFYDD LQDALLDGAV AELKAAGLTH
60 70 80 90 100
DVITVPGALE IPAAVAIAVD AAAANGKPYD AVIALGCVIR GDTIHFEIVS
110 120 130 140 150
QESSRALMDL AVSRKLPLGN GILTVNTEAQ AWARARASEL NKGGDAARAA
160
LAMLRIKRRL ARA
Length:163
Mass (Da):17,094
Last modified:June 1, 2003 - v1
Checksum:i8A3FCDD11A6C181A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC50294.1.
RefSeqiNP_771669.1. NC_004463.1.
WP_011087790.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC50294; BAC50294; BAC50294.
GeneIDi1051859.
KEGGibja:bll5029.
PATRICi21193722. VBIBraJap65052_5106.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC50294.1.
RefSeqiNP_771669.1. NC_004463.1.
WP_011087790.1. NC_004463.1.

3D structure databases

ProteinModelPortaliQ89K80.
SMRiQ89K80. Positions 21-161.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.bll5029.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC50294; BAC50294; BAC50294.
GeneIDi1051859.
KEGGibja:bll5029.
PATRICi21193722. VBIBraJap65052_5106.

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229250.
InParanoidiQ89K80.
KOiK00794.
OMAiTVCNDSS.
OrthoDBiPOG091H021R.
PhylomeDBiQ89K80.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BioCyciBJAP224911:GJEJ-5066-MONOMER.

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 nameiRISB1_BRADU
AccessioniPrimary (citable) accession number: Q89K80
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: June 1, 2003
Last modified: September 7, 2016
This is version 75 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.