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P13000

- BIOD1_ECOLI

UniProt

P13000 - BIOD1_ECOLI

Protein

ATP-dependent dethiobiotin synthetase BioD 1

Gene

bioD1

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 137 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.2 Publications

    Catalytic activityi

    ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin.1 Publication

    Cofactori

    Magnesium.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi13 – 131Magnesium 1
    Metal bindingi17 – 171Magnesium 2
    Binding sitei42 – 421Substrate
    Metal bindingi55 – 551Magnesium 2
    Binding sitei55 – 551ATP
    Metal bindingi116 – 1161Magnesium 2
    Binding sitei212 – 2121ATP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi13 – 186ATP
    Nucleotide bindingi116 – 1194ATP
    Nucleotide bindingi176 – 1772ATP
    Nucleotide bindingi205 – 2073ATP

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB
    2. dethiobiotin synthase activity Source: UniProtKB
    3. magnesium ion binding Source: UniProtKB

    GO - Biological processi

    1. biotin biosynthetic process Source: UniProtKB

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Biotin biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:DETHIOBIOTIN-SYN-MONOMER.
    ECOL316407:JW0761-MONOMER.
    MetaCyc:DETHIOBIOTIN-SYN-MONOMER.
    SABIO-RKP13000.
    UniPathwayiUPA00078; UER00161.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent dethiobiotin synthetase BioD 1 (EC:6.3.3.3)
    Alternative name(s):
    DTB synthetase 1
    Short name:
    DTBS 1
    Dethiobiotin synthase
    Gene namesi
    Name:bioD1
    Ordered Locus Names:b0778, JW0761
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10120. bioD1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi12 – 121T → V: Strong decreased in the affinity for ATP; essential role for this residue in the steady-state affinity for ATP. 1 Publication
    Mutagenesisi13 – 131E → A or D: Almost no change in activity. 1 Publication
    Mutagenesisi16 – 161K → Q: Complete loss of activity. 1 Publication
    Mutagenesisi38 – 381K → L, Q or R: Complete loss of activity. 1 Publication
    Mutagenesisi42 – 421S → A or C: Almost no change in activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 225224ATP-dependent dethiobiotin synthetase BioD 1PRO_0000187961Add
    BLAST

    Proteomic databases

    PaxDbiP13000.
    PRIDEiP13000.

    Expressioni

    Gene expression databases

    GenevestigatoriP13000.

    Interactioni

    Subunit structurei

    Homodimer.6 Publications

    Protein-protein interaction databases

    IntActiP13000. 3 interactions.
    STRINGi511145.b0778.

    Structurei

    Secondary structure

    1
    225
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 119
    Helixi16 – 2914
    Beta strandi34 – 374
    Beta strandi39 – 435
    Beta strandi45 – 473
    Beta strandi50 – 523
    Helixi54 – 618
    Beta strandi63 – 653
    Helixi69 – 724
    Beta strandi74 – 796
    Helixi83 – 908
    Helixi96 – 10712
    Beta strandi111 – 1166
    Beta strandi118 – 1203
    Beta strandi124 – 1263
    Helixi131 – 1388
    Beta strandi142 – 1476
    Helixi152 – 16514
    Beta strandi170 – 1767
    Helixi185 – 19511
    Beta strandi196 – 1983
    Beta strandi200 – 2045
    Turni211 – 2133
    Helixi217 – 2193
    Helixi222 – 2243

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A82X-ray1.80A2-225[»]
    1BS1X-ray1.80A2-225[»]
    1BYIX-ray0.97A2-225[»]
    1DADX-ray1.60A2-225[»]
    1DAEX-ray1.70A2-225[»]
    1DAFX-ray1.70A2-225[»]
    1DAGX-ray1.64A2-225[»]
    1DAHX-ray1.64A2-225[»]
    1DAIX-ray1.64A2-225[»]
    1DAKX-ray1.60A2-225[»]
    1DAMX-ray1.80A2-225[»]
    1DBSX-ray1.80A2-225[»]
    1DTSX-ray1.65A1-224[»]
    ProteinModelPortaliP13000.
    SMRiP13000. Positions 2-225.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13000.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the dethiobiotin synthetase family.Curated

    Phylogenomic databases

    eggNOGiCOG0132.
    HOGENOMiHOG000275032.
    KOiK01935.
    OMAiCINHAVL.
    OrthoDBiEOG66B3XT.
    PhylomeDBiP13000.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00336. BioD.
    InterProiIPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
    IPR004472. DTB_synth_BioD.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF01656. CbiA. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006755. DTB_synth. 1 hit.
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00347. bioD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P13000-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKRYFVTGT DTEVGKTVAS CALLQAAKAA GYRTAGYKPV ASGSEKTPEG    50
    LRNSDALALQ RNSSLQLDYA TVNPYTFAEP TSPHIISAQE GRPIESLVMS 100
    AGLRALEQQA DWVLVEGAGG WFTPLSDTFT FADWVTQEQL PVILVVGVKL 150
    GCINHAMLTA QVIQHAGLTL AGWVANDVTP PGKRHAEYMT TLTRMIPAPL 200
    LGEIPWLAEN PENAATGKYI NLALL 225
    Length:225
    Mass (Da):24,140
    Last modified:January 23, 2007 - v3
    Checksum:i9AE76F3BE6565780
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti29 – 291A → R in AAA23518. (PubMed:3058702)Curated
    Sequence conflicti108 – 1092QQ → HK in CAA00967. 1 PublicationCurated
    Sequence conflicti198 – 22528APLLG…NLALL → RRCWERSPGLQKIQKMRQPE ST in AAA23518. (PubMed:3058702)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J04423 Genomic DNA. Translation: AAA23518.1.
    S68059 Genomic DNA. Translation: AAB29683.2.
    A11538 Unassigned DNA. Translation: CAA00967.1.
    U00096 Genomic DNA. Translation: AAC73865.1.
    AP009048 Genomic DNA. Translation: BAE76365.1.
    PIRiB64814. SYECDB.
    RefSeqiNP_415299.1. NC_000913.3.
    YP_489051.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73865; AAC73865; b0778.
    BAE76365; BAE76365; BAE76365.
    GeneIDi12930962.
    945387.
    KEGGiecj:Y75_p0751.
    eco:b0778.
    PATRICi32116757. VBIEscCol129921_0804.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J04423 Genomic DNA. Translation: AAA23518.1 .
    S68059 Genomic DNA. Translation: AAB29683.2 .
    A11538 Unassigned DNA. Translation: CAA00967.1 .
    U00096 Genomic DNA. Translation: AAC73865.1 .
    AP009048 Genomic DNA. Translation: BAE76365.1 .
    PIRi B64814. SYECDB.
    RefSeqi NP_415299.1. NC_000913.3.
    YP_489051.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1A82 X-ray 1.80 A 2-225 [» ]
    1BS1 X-ray 1.80 A 2-225 [» ]
    1BYI X-ray 0.97 A 2-225 [» ]
    1DAD X-ray 1.60 A 2-225 [» ]
    1DAE X-ray 1.70 A 2-225 [» ]
    1DAF X-ray 1.70 A 2-225 [» ]
    1DAG X-ray 1.64 A 2-225 [» ]
    1DAH X-ray 1.64 A 2-225 [» ]
    1DAI X-ray 1.64 A 2-225 [» ]
    1DAK X-ray 1.60 A 2-225 [» ]
    1DAM X-ray 1.80 A 2-225 [» ]
    1DBS X-ray 1.80 A 2-225 [» ]
    1DTS X-ray 1.65 A 1-224 [» ]
    ProteinModelPortali P13000.
    SMRi P13000. Positions 2-225.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P13000. 3 interactions.
    STRINGi 511145.b0778.

    Proteomic databases

    PaxDbi P13000.
    PRIDEi P13000.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73865 ; AAC73865 ; b0778 .
    BAE76365 ; BAE76365 ; BAE76365 .
    GeneIDi 12930962.
    945387.
    KEGGi ecj:Y75_p0751.
    eco:b0778.
    PATRICi 32116757. VBIEscCol129921_0804.

    Organism-specific databases

    EchoBASEi EB0118.
    EcoGenei EG10120. bioD1.

    Phylogenomic databases

    eggNOGi COG0132.
    HOGENOMi HOG000275032.
    KOi K01935.
    OMAi CINHAVL.
    OrthoDBi EOG66B3XT.
    PhylomeDBi P13000.

    Enzyme and pathway databases

    UniPathwayi UPA00078 ; UER00161 .
    BioCyci EcoCyc:DETHIOBIOTIN-SYN-MONOMER.
    ECOL316407:JW0761-MONOMER.
    MetaCyc:DETHIOBIOTIN-SYN-MONOMER.
    SABIO-RK P13000.

    Miscellaneous databases

    EvolutionaryTracei P13000.
    PROi P13000.

    Gene expression databases

    Genevestigatori P13000.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    HAMAPi MF_00336. BioD.
    InterProi IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
    IPR004472. DTB_synth_BioD.
    IPR027417. P-loop_NTPase.
    [Graphical view ]
    Pfami PF01656. CbiA. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF006755. DTB_synth. 1 hit.
    SUPFAMi SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR00347. bioD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon."
      Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.
      J. Biol. Chem. 263:19577-19585(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis."
      Alexeev D., Bury S.M., Boys C.W.G., Turner M.A., Sawyer L., Ramsey A.J., Baxter H.C., Baxter R.L.
      J. Mol. Biol. 235:774-776(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20 AND 224-225.
    3. "Genetic material for expression of biotin synthetase enzymes."
      Pearson B.M., McKee R.A.
      Patent number GB2216530, 11-OCT-1989
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    6. "Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12."
      Eisenberg M.A., Krell K.
      J. Bacteriol. 98:1227-1231(1969) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN BIOTIN BIOSYNTHESIS.
    7. "The purification and properties of dethiobiotin synthetase."
      Krell K., Eisenberg M.A.
      J. Biol. Chem. 245:6558-6566(1970) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A DETHIOBIOTIN SYNTHETASE, CATALYTIC ACTIVITY, SUBSTRATES SPECIFICITY, SUBUNIT.
    8. "Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties."
      Yang G., Sandalova T., Lohman K., Lindqvist Y., Rendina A.R.
      Biochemistry 36:4751-4760(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF THR-12; GLU-13; LYS-16; LYS-38 AND SER-42.
    9. "Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65-A resolution."
      Huang W., Lindqvist Y., Schneider G., Gibson K.J., Flint D., Lorimer G.
      Structure 2:407-414(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), SUBUNIT.
    10. "Mechanistic implications and family relationships from the structure of dethiobiotin synthetase."
      Sawyer L., Baxter R.L., Alexeev D.
      Structure 2:1061-1072(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, SUBUNIT.
    11. "Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate."
      Huang W., Jia J., Gibson K.J., Taylor W.S., Rendina A.R., Schneider G., Lindqvist Y.
      Biochemistry 34:10985-10995(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 2-224 IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, REACTION MECHANISM.
    12. "Snapshot of a phosphorylated substrate intermediate by kinetic crystallography."
      Kaeck H., Gibson K.J., Lindqvist Y., Schneider G.
      Proc. Natl. Acad. Sci. U.S.A. 95:5495-5500(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP, MAGNESIUM IONS.
    13. "Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis."
      Kaeck H., Sandmark J., Gibson K.J., Schneider G., Lindqvist Y.
      Protein Sci. 7:2560-2566(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, SUBUNIT.
    14. "Structure of dethiobiotin synthetase at 0.97-A resolution."
      Sandalova T., Schneider G., Kack H., Lindqvist Y.
      Acta Crystallogr. D 55:610-624(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS).

    Entry informationi

    Entry nameiBIOD1_ECOLI
    AccessioniPrimary (citable) accession number: P13000
    Secondary accession number(s): Q2MBJ1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 137 of the entry and version 3 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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