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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)DescriptionActionsGraphical viewLength
    Binding sitei59FMN; via amide nitrogen1
    Binding sitei108FMN; via carbonyl oxygen1
    Binding sitei167FMN1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi30 – 34FMN5

    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.
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi32D → A, N or S: Abrogates DMB formation but retains flavin binding. 1 Publication1
    Mutagenesisi167S → C: Completely abolishes DMB formation. 1 Publication1
    Mutagenesisi167S → G: Reduces DMB formation by 30-fold. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004240851 – 2275,6-dimethylbenzimidazole synthaseAdd BLAST227

    Interactioni

    Subunit structurei

    Homooctamer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-60275N.
    STRINGi266834.SMc00166.

    Structurei

    Secondary structure

    1227
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi17 – 29Combined sources13
    Helixi44 – 55Combined sources12
    Helixi60 – 62Combined sources3
    Beta strandi66 – 71Combined sources6
    Helixi74 – 93Combined sources20
    Helixi97 – 105Combined sources9
    Turni111 – 113Combined sources3
    Beta strandi114 – 123Combined sources10
    Turni124 – 127Combined sources4
    Helixi140 – 159Combined sources20
    Beta strandi161 – 165Combined sources5
    Helixi171 – 178Combined sources8
    Beta strandi184 – 194Combined sources11
    Beta strandi196 – 198Combined sources3
    Helixi203 – 206Combined sources4
    Helixi215 – 218Combined sources4
    Beta strandi219 – 223Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    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

    CDDicd02145. BluB. 1 hit.
    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
    PDB 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.
    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.
    BRENDAi1.14.99.40. 5347.

    Miscellaneous databases

    EvolutionaryTraceiQ92PC8.

    Family and domain databases

    CDDicd02145. BluB. 1 hit.
    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: November 2, 2016
    This is version 87 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.