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Q60364

- RIBB_METJA

UniProt

Q60364 - RIBB_METJA

Protein

3,4-dihydroxy-2-butanone 4-phosphate synthase

Gene

ribB

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 1 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.1 Publication

    Catalytic activityi

    D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.

    Cofactori

    Binds 2 divalent metal cations per subunit. Magnesium or manganese.1 Publication

    Kineticsi

    1. KM=140 µM for ribulose-5-phosphate1 Publication

    Vmax=148 nmol/min/mg enzyme1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi26 – 261Magnesium or manganese 1
    Metal bindingi26 – 261Magnesium or manganese 2
    Binding sitei30 – 301Substrate2 Publications
    Sitei147 – 1471Essential for catalytic activity
    Metal bindingi164 – 1641Magnesium or manganese 2
    Binding sitei185 – 1851Substrate2 Publications
    Sitei185 – 1851Essential for catalytic activity

    GO - Molecular functioni

    1. 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: UniProtKB-HAMAP
    2. magnesium ion binding Source: UniProtKB-HAMAP
    3. manganese ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. riboflavin biosynthetic process Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Riboflavin biosynthesis

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14603.
    UniPathwayiUPA00275; UER00399.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3,4-dihydroxy-2-butanone 4-phosphate synthase (EC:4.1.99.12)
    Short name:
    DHBP synthase
    Gene namesi
    Name:ribB
    Ordered Locus Names:MJ0055
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    ProteomesiUP000000805: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi21 – 211D → E or N: Loss of activity. 1 Publication
    Mutagenesisi21 – 211D → S: Reduces activity 70-fold. 1 Publication
    Mutagenesisi25 – 251R → E or K: Reduces activity 50-fold. 1 Publication
    Mutagenesisi26 – 261E → D, Q or S: Loss of activity. 1 Publication
    Mutagenesisi28 – 281E → D or S: Loss of activity. 1 Publication
    Mutagenesisi28 – 281E → Q: Reduces activity 23-fold. 1 Publication
    Mutagenesisi30 – 301D → E or N: Loss of activity. 1 Publication
    Mutagenesisi30 – 301D → S: Reduces activity 30-fold. 1 Publication
    Mutagenesisi55 – 551C → G: Reduces activity 70-fold. Increases Km for ribulose-5-phosphate 7-fold. 1 Publication
    Mutagenesisi55 – 551C → S: Reduces activity 30-fold. 1 Publication
    Mutagenesisi112 – 1121T → A: Reduces activity 50-fold. Increases Km for ribulose-5-phosphate 10-fold. 1 Publication
    Mutagenesisi119 – 1191R → S: Reduces activity 8-fold. Increases Km for ribulose-5-phosphate 8-fold. 1 Publication
    Mutagenesisi147 – 1471H → S: Reduces activity 10-fold.
    Mutagenesisi161 – 1611R → S: Reduces activity 10-fold. Increases Km for ribulose-5-phosphate 7-fold. 1 Publication
    Mutagenesisi164 – 1641H → N or S: Loss of activity. 1 Publication
    Mutagenesisi165 – 1651T → A: Reduces activity by 2-fold. Increases Km for ribulose-5-phosphate 8-fold. 1 Publication
    Mutagenesisi165 – 1651T → S: Reduces activity by 3-fold. 1 Publication
    Mutagenesisi166 – 1661E → S: Increases Km for ribulose-5-phosphate 8-fold. 1 Publication
    Mutagenesisi185 – 1851E → D, Q or S: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2272273,4-dihydroxy-2-butanone 4-phosphate synthasePRO_0000151825Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Protein-protein interaction databases

    STRINGi243232.MJ0055.

    Structurei

    Secondary structure

    1
    227
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1210
    Beta strandi17 – 204
    Turni23 – 264
    Beta strandi29 – 346
    Helixi35 – 373
    Helixi40 – 4910
    Beta strandi51 – 588
    Helixi60 – 667
    Helixi71 – 788
    Turni79 – 813
    Helixi83 – 875
    Beta strandi96 – 983
    Beta strandi101 – 1077
    Beta strandi111 – 1133
    Helixi116 – 13116
    Helixi135 – 1373
    Helixi138 – 1414
    Beta strandi142 – 15211
    Helixi157 – 1593
    Helixi164 – 17411
    Beta strandi179 – 1879
    Beta strandi191 – 1933
    Helixi196 – 20611
    Beta strandi210 – 2123
    Helixi213 – 2197

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PVWX-ray2.45A/B/C1-227[»]
    1PVYX-ray1.70A/B1-227[»]
    1SNNX-ray1.55A/B1-227[»]
    ProteinModelPortaliQ60364.
    SMRiQ60364. Positions 2-220.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ60364.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni25 – 262Substrate binding
    Regioni161 – 1655Substrate binding

    Sequence similaritiesi

    Belongs to the DHBP synthase family.Curated

    Phylogenomic databases

    eggNOGiCOG0108.
    KOiK02858.
    OMAiQMAKLIR.
    PhylomeDBiQ60364.

    Family and domain databases

    Gene3Di3.90.870.10. 1 hit.
    HAMAPiMF_00180. RibB.
    InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
    IPR000422. DHBP_synthase_RibB.
    [Graphical view]
    PfamiPF00926. DHBP_synthase. 1 hit.
    [Graphical view]
    SUPFAMiSSF55821. SSF55821. 1 hit.
    TIGRFAMsiTIGR00506. ribB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q60364-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNNVEKAIEA LKKGEIILVY DSDEREGETD MVVASQFITP EHIRIMRKDA    50
    GGLICTALHP DICNKLGIPF MVDILEFASQ KFKVLRELYP NDIPYDEKSS 100
    FSITINHRKT FTGITDNDRA FTIKKLAELV KEGRFNDFGK EFRSPGHVTL 150
    LRAAEGLVKN RQGHTEMTVA LAELANLVPI TTICEMMGDD GNAMSKNETK 200
    RYAEKHNLIY LSGEEIINYY LDKYLKD 227
    Length:227
    Mass (Da):25,797
    Last modified:November 1, 1997 - v1
    Checksum:i0718EE5B4247995D
    GO

    Mass spectrometryi

    Molecular mass is 25799 Da from positions 1 - 227. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L77117 Genomic DNA. Translation: AAB98035.1.
    PIRiG64306.
    RefSeqiNP_247019.1. NC_000909.1.
    WP_010869547.1. NC_000909.1.

    Genome annotation databases

    EnsemblBacteriaiAAB98035; AAB98035; MJ_0055.
    GeneIDi1450894.
    KEGGimja:MJ_0055.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L77117 Genomic DNA. Translation: AAB98035.1 .
    PIRi G64306.
    RefSeqi NP_247019.1. NC_000909.1.
    WP_010869547.1. NC_000909.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1PVW X-ray 2.45 A/B/C 1-227 [» ]
    1PVY X-ray 1.70 A/B 1-227 [» ]
    1SNN X-ray 1.55 A/B 1-227 [» ]
    ProteinModelPortali Q60364.
    SMRi Q60364. Positions 2-220.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243232.MJ0055.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAB98035 ; AAB98035 ; MJ_0055 .
    GeneIDi 1450894.
    KEGGi mja:MJ_0055.

    Phylogenomic databases

    eggNOGi COG0108.
    KOi K02858.
    OMAi QMAKLIR.
    PhylomeDBi Q60364.

    Enzyme and pathway databases

    UniPathwayi UPA00275 ; UER00399 .
    BioCyci MetaCyc:MONOMER-14603.

    Miscellaneous databases

    EvolutionaryTracei Q60364.

    Family and domain databases

    Gene3Di 3.90.870.10. 1 hit.
    HAMAPi MF_00180. RibB.
    InterProi IPR017945. DHBP_synth_RibB-like_a/b_dom.
    IPR000422. DHBP_synthase_RibB.
    [Graphical view ]
    Pfami PF00926. DHBP_synthase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55821. SSF55821. 1 hit.
    TIGRFAMsi TIGR00506. ribB. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
    2. "Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii."
      Fischer M., Roemisch W., Schiffmann S., Kelly M., Oschkinat H., Steinbacher S., Huber R., Eisenreich W., Richter G., Bacher A.
      J. Biol. Chem. 277:41410-41416(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-15, FUNCTION, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, COFACTOR, MUTAGENESIS OF ASP-21; ARG-25; GLU-26; GLU-28; ASP-30; CYS-55; THR-112; ARG-119; ARG-161; HIS-164; THR-165; GLU-166 AND GLU-185.
    3. "Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism."
      Steinbacher S., Schiffmann S., Richter G., Huber R., Bacher A., Fischer M.
      J. Biol. Chem. 278:42256-42265(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF MUTANT SER-147 IN COMPLEX WITH DIVALENT METAL CATIONS AND SUBSTRATE, SUBUNIT.
    4. "Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate."
      Steinbacher S., Schiffmann S., Bacher A., Fischer M.
      Acta Crystallogr. D 60:1338-1340(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF MUTANT SER-147 IN COMPLEX WITH DIVALENT METAL CATIONS AND SUBSTRATE, SUBUNIT.

    Entry informationi

    Entry nameiRIBB_METJA
    AccessioniPrimary (citable) accession number: Q60364
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 91 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, Direct protein sequencing, Reference proteome

    Documents

    1. Methanococcus jannaschii
      Methanococcus jannaschii: 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

    External Data

    Dasty 3