Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribH

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 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. Is able to use the non-natural R enantiomer of 3,4-dihydroxy-2-butanone 4-phosphate as a substrate, but with less efficiency than the natural S enantiomer. Cannot use unphosphorylated 3,4-dihydroxy-2-butanone, 3,4-dihydroxy-2-butanone 3-phosphate or diacetyl as substrates.2 Publications

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.2 Publications

Kineticsi

kcat is 0.056 sec(-1).1 Publication

Manual assertion based on experiment ini

  1. KM=5 µM for 5-amino-6-(D-ribitylamino)uracil2 Publications
  2. KM=9 µM for 5-amino-6-(D-ribitylamino)uracil2 Publications
  3. KM=130 µM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate2 Publications
  4. KM=55 µM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate2 Publications
  1. Vmax=12000 nmol/h/mg enzyme2 Publications

pH dependencei

Optimum pH is 6.5-8.0.1 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 (ribH)
  2. Riboflavin synthase (ribE)
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
Active sitei88Proton donorSequence analysis1
Binding sitei1135-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen1
Binding sitei1271-deoxy-L-glycero-tetrulose 4-phosphateCurated1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciBSUB:BSU23250-MONOMER.
MetaCyc:MONOMER-14609.
BRENDAi2.5.1.78. 658.
SABIO-RKP11998.
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
Alternative name(s):
Heavy riboflavin synthase beta subunit
Short name:
HRS beta subunit
Gene namesi
Name:ribH
Ordered Locus Names:BSU23250
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi88H → A: 10% of wild-type activity. 17-fold decrease in the affinity for the pyrimidine substrate, but no effect on that for 1-deoxy-L-glycero-tetrulose 4-phosphate. 1 Publication1
Mutagenesisi127R → T: About 1% of wild-type activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001347151 – 1546,7-dimethyl-8-ribityllumazine synthaseAdd BLAST154

Proteomic databases

PaxDbiP11998.
PRIDEiP11998.

Interactioni

Subunit structurei

Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Can interact with riboflavin synthase, forming a lumazine synthase/riboflavin synthase complex, also designated as 'heavy riboflavin synthase complex', which consists of a trimer of riboflavin synthase enclosed within the icosahedral structure composed of 60 subunits of 6,7-dimethyl-8-ribityllumazine synthase.4 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012766.

Structurei

Secondary structure

1154
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Beta strandi15 – 21Combined sources7
Helixi24 – 40Combined sources17
Helixi45 – 47Combined sources3
Beta strandi48 – 55Combined sources8
Helixi56 – 58Combined sources3
Helixi59 – 68Combined sources10
Beta strandi73 – 82Combined sources10
Beta strandi85 – 87Combined sources3
Helixi88 – 107Combined sources20
Beta strandi111 – 120Combined sources10
Helixi121 – 126Combined sources6
Beta strandi128 – 130Combined sources3
Helixi135 – 152Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RVVX-ray2.401/2/3/4/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z1-154[»]
1ZISX-ray2.90A/B/C/D/E/F/G/H/I/J1-154[»]
ProteinModelPortaliP11998.
SMRiP11998.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11998.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni22 – 235-amino-6-(D-ribitylamino)uracil binding2
Regioni56 – 585-amino-6-(D-ribitylamino)uracil binding3
Regioni80 – 825-amino-6-(D-ribitylamino)uracil binding3
Regioni85 – 861-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated2

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229249.
InParanoidiP11998.
KOiK00794.
OMAiCDTVDQA.
PhylomeDBiP11998.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

P11998-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIIQGNLVG TGLKIGIVVG RFNDFITSKL LSGAEDALLR HGVDTNDIDV
60 70 80 90 100
AWVPGAFEIP FAAKKMAETK KYDAIITLGT VIRGATTHYD YVCNEAAKGI
110 120 130 140 150
AQAANTTGVP VIFGIVTTEN IEQAIERAGT KAGNKGVDCA VSAIEMANLN

RSFE
Length:154
Mass (Da):16,287
Last modified:February 1, 1994 - v2
Checksum:i76CB336DF6A4BFEB
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti65K → G AA sequence (PubMed:3100522).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09228 Genomic DNA. Translation: AAA67484.1.
X51510 Genomic DNA. Translation: CAA35881.1.
AF516949 Genomic DNA. Translation: AAN01132.1.
AL009126 Genomic DNA. Translation: CAB14257.1.
PIRiS45546. A26708.
RefSeqiNP_390206.1. NC_000964.3.
WP_003223915.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14257; CAB14257; BSU23250.
GeneIDi11239989.
938949.
KEGGibsu:BSU23250.
PATRICi18976467. VBIBacSub10457_2424.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09228 Genomic DNA. Translation: AAA67484.1.
X51510 Genomic DNA. Translation: CAA35881.1.
AF516949 Genomic DNA. Translation: AAN01132.1.
AL009126 Genomic DNA. Translation: CAB14257.1.
PIRiS45546. A26708.
RefSeqiNP_390206.1. NC_000964.3.
WP_003223915.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RVVX-ray2.401/2/3/4/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z1-154[»]
1ZISX-ray2.90A/B/C/D/E/F/G/H/I/J1-154[»]
ProteinModelPortaliP11998.
SMRiP11998.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012766.

Proteomic databases

PaxDbiP11998.
PRIDEiP11998.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14257; CAB14257; BSU23250.
GeneIDi11239989.
938949.
KEGGibsu:BSU23250.
PATRICi18976467. VBIBacSub10457_2424.

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229249.
InParanoidiP11998.
KOiK00794.
OMAiCDTVDQA.
PhylomeDBiP11998.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BioCyciBSUB:BSU23250-MONOMER.
MetaCyc:MONOMER-14609.
BRENDAi2.5.1.78. 658.
SABIO-RKP11998.

Miscellaneous databases

EvolutionaryTraceiP11998.

Family and domain databases

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

Entry informationi

Entry nameiRISB_BACSU
AccessioniPrimary (citable) accession number: P11998
Secondary accession number(s): P17621
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: February 1, 1994
Last modified: November 2, 2016
This is version 133 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, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.