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P11998 (RISB_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
6,7-dimethyl-8-ribityllumazine synthase

Short name=DMRL synthase
Short name=LS
Short name=Lumazine synthase
EC=2.5.1.78
Alternative name(s):
Heavy riboflavin synthase beta subunit
Short name=HRS beta subunit
Gene names
Name:ribH
Ordered Locus Names:BSU23250
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length154 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.8

Catalytic activity

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

Pathway

Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Ref.8

Subunit structure

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. Ref.7 Ref.9 Ref.10

Sequence similarities

Belongs to the DMRL synthase family.

Biophysicochemical properties

Kinetic parameters:

kcat is 0.056 sec(-1) (Ref.4).

KM=5 µM for 5-amino-6-(D-ribitylamino)uracil (Ref.8) Ref.4 Ref.8

KM=9 µM for 5-amino-6-(D-ribitylamino)uracil (Ref.4)

KM=130 µM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate (Ref.8)

KM=55 µM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate (Ref.4)

Vmax=12000 nmol/h/mg enzyme (Ref.8)

pH dependence:

Optimum pH is 6.5-8.0.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 1541546,7-dimethyl-8-ribityllumazine synthase HAMAP-Rule MF_00178
PRO_0000134715

Regions

Region22 – 2325-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178
Region56 – 5835-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178
Region80 – 8235-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178
Region85 – 8621-deoxy-L-glycero-tetrulose 4-phosphate binding Probable

Sites

Active site881Proton donor Potential
Binding site11315-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen
Binding site12711-deoxy-L-glycero-tetrulose 4-phosphate Probable

Experimental info

Mutagenesis881H → 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. Ref.4
Mutagenesis1271R → T: About 1% of wild-type activity. Ref.4
Sequence conflict651K → G AA sequence Ref.1

Secondary structure

........................ 154
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P11998 [UniParc].

Last modified February 1, 1994. Version 2.
Checksum: 76CB336DF6A4BFEB

FASTA15416,287
        10         20         30         40         50         60 
MNIIQGNLVG TGLKIGIVVG RFNDFITSKL LSGAEDALLR HGVDTNDIDV AWVPGAFEIP 

        70         80         90        100        110        120 
FAAKKMAETK KYDAIITLGT VIRGATTHYD YVCNEAAKGI AQAANTTGVP VIFGIVTTEN 

       130        140        150 
IEQAIERAGT KAGNKGVDCA VSAIEMANLN RSFE 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L09228 Genomic DNA. Translation: AAA67484.1.
X51510 Genomic DNA. Translation: CAA35881.1.
AF516949 Genomic DNA. Translation: AAN01132.1.
AL009126 Genomic DNA. Translation: CAB14257.1.
PIRA26708. S45546.
RefSeqNP_390206.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP11998.
SMRP11998. Positions 1-154.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU23250.

Proteomic databases

PaxDbP11998.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB14257; CAB14257; BSU23250.
GeneID938949.
KEGGbsu:BSU23250.
PATRIC18976467. VBIBacSub10457_2424.

Organism-specific databases

GenoListBSU23250. [Micado]

Phylogenomic databases

eggNOGCOG0054.
HOGENOMHOG000229249.
KOK00794.
OMAGRFNSFI.
OrthoDBEOG6RC3WC.
ProtClustDBPRK00061.

Enzyme and pathway databases

BioCycBSUB:BSU23250-MONOMER.
MetaCyc:MONOMER-14609.
SABIO-RKP11998.
UniPathwayUPA00275; UER00404.

Family and domain databases

Gene3D3.40.50.960. 1 hit.
HAMAPMF_00178. Lumazine_synth.
InterProIPR002180. DMRL_synthase.
[Graphical view]
PANTHERPTHR21058. PTHR21058. 1 hit.
PfamPF00885. DMRL_synthase. 1 hit.
[Graphical view]
SUPFAMSSF52121. SSF52121. 1 hit.
TIGRFAMsTIGR00114. lumazine-synth. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP11998.

Entry information

Entry nameRISB_BACSU
AccessionPrimary (citable) accession number: P11998
Secondary accession number(s): P17621
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: February 1, 1994
Last modified: February 19, 2014
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Bacillus subtilis

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