Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P11998

- RISB_BACSU

UniProt

P11998 - RISB_BACSU

Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribH

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 2 (01 Feb 1994)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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

    Vmax=12000 nmol/h/mg enzyme2 Publications

    pH dependencei

    Optimum pH is 6.5-8.0.1 Publication

    Pathwayi

    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

    1. 6,7-dimethyl-8-ribityllumazine synthase activity Source: UniProtKB-HAMAP
    2. transferase activity Source: UniProtKB-KW

    GO - Biological processi

    1. riboflavin biosynthetic process Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Riboflavin biosynthesis

    Enzyme and pathway databases

    BioCyciBSUB:BSU23250-MONOMER.
    MetaCyc:MONOMER-14609.
    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: Chromosome

    Organism-specific databases

    GenoListiBSU23250. [Micado]

    Subcellular locationi

    GO - Cellular componenti

    1. riboflavin synthase complex Source: InterPro

    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.BSU23250.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK00794.
    OMAiIEMANLS.
    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

    MNIIQGNLVG TGLKIGIVVG RFNDFITSKL LSGAEDALLR HGVDTNDIDV    50
    AWVPGAFEIP FAAKKMAETK KYDAIITLGT VIRGATTHYD YVCNEAAKGI 100
    AQAANTTGVP VIFGIVTTEN IEQAIERAGT KAGNKGVDCA VSAIEMANLN 150
    RSFE 154
    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:
    EMBL
    GenBank
    DDBJ
    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.

    Genome annotation databases

    EnsemblBacteriaiCAB14257; CAB14257; BSU23250.
    GeneIDi938949.
    KEGGibsu:BSU23250.
    PATRICi18976467. VBIBacSub10457_2424.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi S45546. A26708.
    RefSeqi NP_390206.1. NC_000964.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1RVV X-ray 2.40 1/2/3/4/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/Z 1-154 [» ]
    1ZIS X-ray 2.90 A/B/C/D/E/F/G/H/I/J 1-154 [» ]
    ProteinModelPortali P11998.
    SMRi P11998. Positions 1-154.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU23250.

    Proteomic databases

    PaxDbi P11998.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB14257 ; CAB14257 ; BSU23250 .
    GeneIDi 938949.
    KEGGi bsu:BSU23250.
    PATRICi 18976467. VBIBacSub10457_2424.

    Organism-specific databases

    GenoListi BSU23250. [Micado ]

    Phylogenomic databases

    eggNOGi COG0054.
    HOGENOMi HOG000229249.
    KOi K00794.
    OMAi IEMANLS.
    OrthoDBi EOG6RC3WC.
    PhylomeDBi P11998.

    Enzyme and pathway databases

    UniPathwayi UPA00275 ; UER00404 .
    BioCyci BSUB:BSU23250-MONOMER.
    MetaCyc:MONOMER-14609.
    SABIO-RK P11998.

    Miscellaneous databases

    EvolutionaryTracei P11998.

    Family and domain databases

    Gene3Di 3.40.50.960. 1 hit.
    HAMAPi MF_00178. Lumazine_synth.
    InterProi IPR002180. DMRL_synthase.
    [Graphical view ]
    PANTHERi PTHR21058. PTHR21058. 1 hit.
    Pfami PF00885. DMRL_synthase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52121. SSF52121. 1 hit.
    TIGRFAMsi TIGR00114. lumazine-synth. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 120 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