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Protein

5,6-dimethylbenzimidazole synthase

Gene

bluB

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of cobalamin (vitamin B12). Catalyzes the oxidative fragmentation and contraction of the isoalloxazine heterocycle and the cleavage of the ribityl tail of FMN2 to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-phosphate (E4P). NAD(P)H is only required initially to reduce FMN and oxygen drives the oxidative fragmentation.2 Publications

Catalytic activityi

FMNH2 + NADH + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + other product(s).1 Publication

Enzyme regulationi

Inhibited by high concentrations of FMN.1 Publication

Kineticsi

Kcat is 15 (h-1), 7.2 (h-1) and 7.6 (h-1) for FMN, NAD and NADP, respectively.

  1. KM=64 µM for FMN1 Publication
  2. KM=4.4 mM for NADP1 Publication
  3. KM=5.1 mM for NAD1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei59 – 591FMN; via amide nitrogen
    Binding sitei108 – 1081FMN; via carbonyl oxygen
    Binding sitei167 – 1671FMN

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi30 – 345FMN

    GO - Molecular functioni

    GO - Biological processi

    • cobalamin biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Cobalamin biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN, NAD, NADP, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13177.
    SMEL266834:GJF6-1889-MONOMER.
    BRENDAi1.14.99.40. 5347.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    5,6-dimethylbenzimidazole synthase (EC:1.13.11.79)
    Short name:
    DMB synthase
    Gene namesi
    Name:bluB
    Ordered Locus Names:R01841
    ORF Names:SMc00166
    OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
    Taxonomic identifieri266834 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
    Proteomesi
    • UP000001976 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene are unable to grow in minimal media and fails to establish a symbiosis with alfalfa, and these defects can be rescued by the addition of vitamin B12 (cyanocobalamin) or the lower ligand of cobalamin, 5,6-dimethylbenzimidazole (DMB).1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi32 – 321D → A, N or S: Abrogates DMB formation but retains flavin binding. 1 Publication
    Mutagenesisi167 – 1671S → C: Completely abolishes DMB formation. 1 Publication
    Mutagenesisi167 – 1671S → G: Reduces DMB formation by 30-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2272275,6-dimethylbenzimidazole synthasePRO_0000424085Add
    BLAST

    Interactioni

    Subunit structurei

    Homooctamer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-60275N.
    STRINGi266834.SMc00166.

    Structurei

    Secondary structure

    1
    227
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi17 – 2913Combined sources
    Helixi44 – 5512Combined sources
    Helixi60 – 623Combined sources
    Beta strandi66 – 716Combined sources
    Helixi74 – 9320Combined sources
    Helixi97 – 1059Combined sources
    Turni111 – 1133Combined sources
    Beta strandi114 – 12310Combined sources
    Turni124 – 1274Combined sources
    Helixi140 – 15920Combined sources
    Beta strandi161 – 1655Combined sources
    Helixi171 – 1788Combined sources
    Beta strandi184 – 19411Combined sources
    Beta strandi196 – 1983Combined sources
    Helixi203 – 2064Combined sources
    Helixi215 – 2184Combined sources
    Beta strandi219 – 2235Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ISJX-ray2.30A/B/C/D/E/F/G/H1-227[»]
    2ISKX-ray2.10A/B/C/D/E/F/G/H1-227[»]
    2ISLX-ray2.90A/B/C/D/E/F/G/H1-227[»]
    ProteinModelPortaliQ92PC8.
    SMRiQ92PC8. Positions 9-227.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ92PC8.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the BluB family.Curated

    Phylogenomic databases

    eggNOGiENOG4105E7Q. Bacteria.
    COG0778. LUCA.
    HOGENOMiHOG000146735.
    KOiK04719.
    OMAiHNPEMDL.

    Family and domain databases

    Gene3Di3.40.109.10. 1 hit.
    InterProiIPR012825. BluB.
    IPR029479. Nitroreductase.
    IPR000415. Nitroreductase-like.
    [Graphical view]
    PfamiPF00881. Nitroreductase. 1 hit.
    [Graphical view]
    SUPFAMiSSF55469. SSF55469. 1 hit.
    TIGRFAMsiTIGR02476. BluB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q92PC8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLPDPNGCLT AAGAFSSDER AAVYRAIETR RDVRDEFLPE PLSEELIARL
    60 70 80 90 100
    LGAAHQAPSV GFMQPWNFVL VRQDETREKV WQAFQRANDE AAEMFSGERQ
    110 120 130 140 150
    AKYRSLKLEG IRKAPLSICV TCDRTRGGAV VLGRTHNPQM DLYSTVCAVQ
    160 170 180 190 200
    NLWLAARAEG VGVGWVSIFH ESEIKAILGI PDHVEIVAWL CLGFVDRLYQ
    210 220
    EPELAAKGWR QRLPLEDLVF EEGWGVR
    Length:227
    Mass (Da):25,508
    Last modified:December 1, 2001 - v1
    Checksum:i68BE6DA9CC4E595F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL591688 Genomic DNA. Translation: CAC46420.1.
    RefSeqiNP_385947.1. NC_003047.1.
    WP_010969508.1. NC_003047.1.

    Genome annotation databases

    EnsemblBacteriaiCAC46420; CAC46420; SMc00166.
    GeneIDi1233506.
    KEGGisme:SMc00166.
    PATRICi23633091. VBISinMel96828_3284.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL591688 Genomic DNA. Translation: CAC46420.1.
    RefSeqiNP_385947.1. NC_003047.1.
    WP_010969508.1. NC_003047.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ISJX-ray2.30A/B/C/D/E/F/G/H1-227[»]
    2ISKX-ray2.10A/B/C/D/E/F/G/H1-227[»]
    2ISLX-ray2.90A/B/C/D/E/F/G/H1-227[»]
    ProteinModelPortaliQ92PC8.
    SMRiQ92PC8. Positions 9-227.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-60275N.
    STRINGi266834.SMc00166.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAC46420; CAC46420; SMc00166.
    GeneIDi1233506.
    KEGGisme:SMc00166.
    PATRICi23633091. VBISinMel96828_3284.

    Phylogenomic databases

    eggNOGiENOG4105E7Q. Bacteria.
    COG0778. LUCA.
    HOGENOMiHOG000146735.
    KOiK04719.
    OMAiHNPEMDL.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13177.
    SMEL266834:GJF6-1889-MONOMER.
    BRENDAi1.14.99.40. 5347.

    Miscellaneous databases

    EvolutionaryTraceiQ92PC8.

    Family and domain databases

    Gene3Di3.40.109.10. 1 hit.
    InterProiIPR012825. BluB.
    IPR029479. Nitroreductase.
    IPR000415. Nitroreductase-like.
    [Graphical view]
    PfamiPF00881. Nitroreductase. 1 hit.
    [Graphical view]
    SUPFAMiSSF55469. SSF55469. 1 hit.
    TIGRFAMsiTIGR02476. BluB. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiBLUB_RHIME
    AccessioniPrimary (citable) accession number: Q92PC8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 16, 2013
    Last sequence update: December 1, 2001
    Last modified: September 7, 2016
    This is version 85 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, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.