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P66038

- RISB_SALTY

UniProt

P66038 - RISB_SALTY

Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribH

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 64 (01 Oct 2014)
      Sequence version 1 (11 Oct 2004)
      Previous versions | rss
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    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 By similarity.By similarity

    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.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei22 – 2215-amino-6-(D-ribitylamino)uracilBy similarity
    Active sitei89 – 891Proton donorSequence Analysis
    Binding sitei114 – 11415-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei128 – 12811-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

    BioCyciSENT99287:GCTI-418-MONOMER.
    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
    Gene namesi
    Name:ribH
    Ordered Locus Names:STM0417
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. riboflavin synthase complex Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 1561566,7-dimethyl-8-ribityllumazine synthasePRO_0000134800Add
    BLAST

    Proteomic databases

    PRIDEiP66038.

    Interactioni

    Subunit structurei

    Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM0417.

    Structurei

    Secondary structure

    1
    156
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 54
    Beta strandi15 – 217
    Helixi24 – 4017
    Beta strandi48 – 569
    Turni57 – 593
    Helixi60 – 7011
    Beta strandi74 – 8310
    Beta strandi86 – 883
    Helixi89 – 10820
    Beta strandi112 – 1209
    Helixi122 – 1287
    Helixi136 – 15217

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3MK3X-ray3.571/2/3/4/5/6/7/8/9/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/a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p/q/r/s/t/u/v/w/x/y1-156[»]
    3NQ4X-ray3.501/2/3/4/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/Z1-156[»]
    ProteinModelPortaliP66038.
    SMRiP66038. Positions 1-155.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni57 – 5935-amino-6-(D-ribitylamino)uracil bindingBy similarity
    Regioni81 – 8335-amino-6-(D-ribitylamino)uracil bindingBy similarity
    Regioni86 – 8721-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated

    Sequence similaritiesi

    Belongs to the DMRL synthase family.Curated

    Phylogenomic databases

    HOGENOMiHOG000229253.
    KOiK00794.
    OMAiISRFNDF.
    OrthoDBiEOG6RC3WC.
    PhylomeDBiP66038.

    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.

    P66038-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNIIKANVAA PDARVAITIA RFNQFINDSL LDGAVDALTR IGQVKDDNIT    50
    VVWVPGAYEL PLATEALAKS GKYDAVVALG TVIRGGTAHF EYVAGGASNG 100
    LASVAQDSGV PVAFGVLTTE SIEQAIERAG TKAGNKGAEA ALTALEMINV 150
    LKAIKA 156
    Length:156
    Mass (Da):16,008
    Last modified:October 11, 2004 - v1
    Checksum:iA19018478C53A294
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE006468 Genomic DNA. Translation: AAL19371.1.
    RefSeqiNP_459412.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL19371; AAL19371; STM0417.
    GeneIDi1251936.
    KEGGistm:STM0417.
    PATRICi32379169. VBISalEnt20916_0446.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE006468 Genomic DNA. Translation: AAL19371.1 .
    RefSeqi NP_459412.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3MK3 X-ray 3.57 1/2/3/4/5/6/7/8/9/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/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 1-156 [» ]
    3NQ4 X-ray 3.50 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 1-156 [» ]
    ProteinModelPortali P66038.
    SMRi P66038. Positions 1-155.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM0417.

    Proteomic databases

    PRIDEi P66038.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL19371 ; AAL19371 ; STM0417 .
    GeneIDi 1251936.
    KEGGi stm:STM0417.
    PATRICi 32379169. VBISalEnt20916_0446.

    Phylogenomic databases

    HOGENOMi HOG000229253.
    KOi K00794.
    OMAi ISRFNDF.
    OrthoDBi EOG6RC3WC.
    PhylomeDBi P66038.

    Enzyme and pathway databases

    UniPathwayi UPA00275 ; UER00404 .
    BioCyci SENT99287:GCTI-418-MONOMER.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    2. "Crystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target."
      Kumar P., Singh M., Karthikeyan S.
      Acta Crystallogr. D 67:131-139(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.50 ANGSTROMS) IN COMPLEX WITH SULFATE, SUBUNIT, PATHWAY.

    Entry informationi

    Entry nameiRISB_SALTY
    AccessioniPrimary (citable) accession number: P66038
    Secondary accession number(s): Q8XFI9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 11, 2004
    Last sequence update: October 11, 2004
    Last modified: October 1, 2014
    This is version 64 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3