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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

  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

Pathway:iriboflavin 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei88 – 881Proton donorSequence Analysis
Binding sitei113 – 11315-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen
Binding sitei127 – 12711-deoxy-L-glycero-tetrulose 4-phosphateCurated

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
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU23250. [Micado]

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi88 – 881H → 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 Publication
Mutagenesisi127 – 1271R → T: About 1% of wild-type activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1541546,7-dimethyl-8-ribityllumazine synthasePRO_0000134715Add
BLAST

Proteomic databases

PaxDbiP11998.

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

1
154
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 43Combined sources
Beta strandi15 – 217Combined sources
Helixi24 – 4017Combined sources
Helixi45 – 473Combined sources
Beta strandi48 – 558Combined sources
Helixi56 – 583Combined sources
Helixi59 – 6810Combined sources
Beta strandi73 – 8210Combined sources
Beta strandi85 – 873Combined sources
Helixi88 – 10720Combined sources
Beta strandi111 – 12010Combined sources
Helixi121 – 1266Combined sources
Beta strandi128 – 1303Combined sources
Helixi135 – 15218Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-154.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11998.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni22 – 2325-amino-6-(D-ribitylamino)uracil binding
Regioni56 – 5835-amino-6-(D-ribitylamino)uracil binding
Regioni80 – 8235-amino-6-(D-ribitylamino)uracil binding
Regioni85 – 8621-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

eggNOGiCOG0054.
HOGENOMiHOG000229249.
InParanoidiP11998.
KOiK00794.
OMAiCDTVDQA.
OrthoDBiEOG6RC3WC.
PhylomeDBiP11998.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth.
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti65 – 651K → G AA sequence (PubMed:3100522).Curated

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
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. Positions 1-154.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012766.

Proteomic databases

PaxDbiP11998.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GenoListiBSU23250. [Micado]

Phylogenomic databases

eggNOGiCOG0054.
HOGENOMiHOG000229249.
InParanoidiP11998.
KOiK00794.
OMAiCDTVDQA.
OrthoDBiEOG6RC3WC.
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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Heavy riboflavin synthase of Bacillus subtilis. Primary structure of the beta subunit."
    Ludwig H.C., Lottspeich F., Henschen A., Ladenstein R., Bacher A.
    J. Biol. Chem. 262:1016-1021(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE.
  2. "The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data."
    Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P.
    Mol. Microbiol. 10:385-395(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  3. Mironov V.N.
    Thesis (1989), USSR Academy of Sciences, Russia
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / SHGW.
  4. "Enzyme catalysis via control of activation entropy: site-directed mutagenesis of 6,7-dimethyl-8-ribityllumazine synthase."
    Fischer M., Haase I., Kis K., Meining W., Ladenstein R., Cushman M., Schramek N., Huber R., Bacher A.
    J. Mol. Biol. 326:783-793(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, MUTAGENESIS OF HIS-88 AND ARG-127, MUTAGENESIS OF OTHER RESIDUES.
  5. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  6. "Cold shock stress-induced proteins in Bacillus subtilis."
    Graumann P., Schroeder K., Schmid R., Marahiel M.A.
    J. Bacteriol. 178:4611-4619(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-20.
    Strain: 168 / JH642.
  7. "Heavy riboflavin synthase from Bacillus subtilis. Quaternary structure and reaggregation."
    Bacher A., Ludwig H.C., Schnepple H., Ben-Shaul Y.
    J. Mol. Biol. 187:75-86(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  8. "Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-dimethyl-8-ribityllumazine synthase."
    Kis K., Volk R., Bacher A.
    Biochemistry 34:2883-2892(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, STEREOSPECIFICITY, REACTION MECHANISM, PATHWAY.
  9. "Heavy riboflavin synthase from Bacillus subtilis. Crystal structure analysis of the icosahedral beta 60 capsid at 3.3-A resolution."
    Ladenstein R., Schneider M., Huber R., Bartunik H.-D., Wilson K., Schott K., Bacher A.
    J. Mol. Biol. 203:1045-1070(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), SUBUNIT.
  10. "Studies on the lumazine synthase/riboflavin synthase complex of Bacillus subtilis: crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue inhibitor at 2.4-A resolution."
    Ritseert K., Huber R., Turk D., Ladenstein R., Schmidt-Baese K., Bacher A.
    J. Mol. Biol. 253:151-167(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG INHIBITOR AND PHOSPHATE, SUBUNIT, ACTIVE SITE, REACTION MECHANISM.
  11. "Crystal structure of recombinant lumazine synthase (hexagonal form)."
    Lopez-Jaramillo F.J.
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG INHIBITOR AND PHOSPHATE.

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: June 24, 2015
This is version 126 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

External Data

Dasty 3

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 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.