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 1

Gene

ribH1

Organism
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Status
Reviewed-Annotation score: Annotation score: 4 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.1 Publication

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.1 Publication

Kineticsi

kcat is 0.003 sec(-1) (at 37 degrees Celsius and pH 7.0).

  1. KM=4 µM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees Celsius and pH 7.0)1 Publication
  2. KM=225 µM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees Celsius and pH 7.0)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.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. 6,7-dimethyl-8-ribityllumazine synthase 1 (ribH1), 6,7-dimethyl-8-ribityllumazine synthase 2 (ribH2)
    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)DescriptionActionsGraphical viewLength
    Binding sitei225-amino-6-(D-ribitylamino)uracil1
    Active sitei90Proton donorSequence analysis1
    Binding sitei1155-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen1
    Binding sitei1291-deoxy-L-glycero-tetrulose 4-phosphateBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Riboflavin biosynthesis

    Enzyme and pathway databases

    UniPathwayiUPA00275; UER00404.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    6,7-dimethyl-8-ribityllumazine synthase 1 (EC:2.5.1.78)
    Short name:
    DMRL synthase 1
    Short name:
    LS 1
    Short name:
    Lumazine synthase 1
    Alternative name(s):
    Type I lumazine synthase
    Gene namesi
    Name:ribH1
    Ordered Locus Names:BMEI1187
    OrganismiBrucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
    Taxonomic identifieri224914 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeBrucella
    Proteomesi
    • UP000000419 Componenti: Chromosome I

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001347261 – 1576,7-dimethyl-8-ribityllumazine synthase 1Add BLAST157

    Expressioni

    Inductioni

    The two ribH genes may be differentially expressed during the Brucella infection cycle. Brucella would use RibH1 for flavin biosynthesis during the extracellular phase and RibH2 during intracellular growth (By similarity).By similarity

    Interactioni

    Subunit structurei

    Homopentamer.1 Publication

    Protein-protein interaction databases

    STRINGi224914.BAWG_1022.

    Structurei

    Secondary structure

    1157
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi14 – 20Combined sources7
    Helixi24 – 41Combined sources18
    Beta strandi44 – 52Combined sources9
    Helixi53 – 55Combined sources3
    Helixi56 – 67Combined sources12
    Turni68 – 70Combined sources3
    Beta strandi75 – 84Combined sources10
    Helixi90 – 108Combined sources19
    Beta strandi112 – 122Combined sources11
    Helixi123 – 130Combined sources8
    Turni132 – 135Combined sources4
    Helixi137 – 154Combined sources18

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2O6HX-ray2.70A/B/C/D/E1-157[»]
    ProteinModelPortaliQ8YGH2.
    SMRiQ8YGH2.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8YGH2.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni53 – 555-amino-6-(D-ribitylamino)uracil binding3
    Regioni82 – 845-amino-6-(D-ribitylamino)uracil binding3
    Regioni87 – 881-deoxy-L-glycero-tetrulose 4-phosphate bindingBy similarity2

    Sequence similaritiesi

    Belongs to the DMRL synthase family.Curated

    Phylogenomic databases

    eggNOGiENOG4108UTT. Bacteria.
    COG0054. LUCA.
    HOGENOMiHOG000229250.
    KOiK00794.
    OMAiTVCNDSS.

    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.

    Q8YGH2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEFLMSKHEA DAPHLLIVEA RFYDDLADAL LDGAKAALDE AGATYDVVTV
    60 70 80 90 100
    PGALEIPATI SFALDGADNG GTEYDGFVAL GTVIRGETYH FDIVSNESCR
    110 120 130 140 150
    ALTDLSVEES IAIGNGILTV ENEEQAWVRA RREDKDKGGF AARAALTMIG

    LRKKFGA
    Length:157
    Mass (Da):16,810
    Last modified:March 1, 2002 - v1
    Checksum:i657DE105E3241275
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE008917 Genomic DNA. Translation: AAL52368.1.
    PIRiAE3400.

    Genome annotation databases

    EnsemblBacteriaiAAL52368; AAL52368; BMEI1187.
    KEGGibme:BMEI1187.
    PATRICi17797634. VBIBruMel146950_0635.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE008917 Genomic DNA. Translation: AAL52368.1.
    PIRiAE3400.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2O6HX-ray2.70A/B/C/D/E1-157[»]
    ProteinModelPortaliQ8YGH2.
    SMRiQ8YGH2.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224914.BAWG_1022.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL52368; AAL52368; BMEI1187.
    KEGGibme:BMEI1187.
    PATRICi17797634. VBIBruMel146950_0635.

    Phylogenomic databases

    eggNOGiENOG4108UTT. Bacteria.
    COG0054. LUCA.
    HOGENOMiHOG000229250.
    KOiK00794.
    OMAiTVCNDSS.

    Enzyme and pathway databases

    UniPathwayiUPA00275; UER00404.

    Miscellaneous databases

    EvolutionaryTraceiQ8YGH2.

    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_BRUME
    AccessioniPrimary (citable) accession number: Q8YGH2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2004
    Last sequence update: March 1, 2002
    Last modified: November 2, 2016
    This is version 89 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

    3D-structure, Complete proteome

    Documents

    1. Brucella melitensis
      Brucella melitensis (strain 16M): entries and gene names
    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.