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O24872

- BIOD_HELPY

UniProt

O24872 - BIOD_HELPY

Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      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.By similarity

    Catalytic activityi

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

    Cofactori

    Magnesium.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi10 – 101Magnesium 1By similarity
    Metal bindingi14 – 141Magnesium 2
    Binding sitei35 – 351ATP
    Binding sitei39 – 391Substrate
    Metal bindingi50 – 501Magnesium 2
    Binding sitei50 – 501ATP
    Binding sitei63 – 631ATP
    Metal bindingi116 – 1161Magnesium 2
    Binding sitei175 – 1751ATP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi9 – 157ATP
    Nucleotide bindingi116 – 1194ATP
    Nucleotide bindingi151 – 1544Substrate

    GO - Molecular functioni

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

    GO - Biological processi

    1. biotin biosynthetic process Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Biotin biosynthesis

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciHPY:HP0029-MONOMER.
    UniPathwayiUPA00078; UER00161.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent dethiobiotin synthetase BioD (EC:6.3.3.3)
    Alternative name(s):
    DTB synthetase
    Short name:
    DTBS
    Dethiobiotin synthase
    Gene namesi
    Name:bioD
    Ordered Locus Names:HP_0029
    OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
    Taxonomic identifieri85962 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
    ProteomesiUP000000429: Chromosome

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 218218ATP-dependent dethiobiotin synthetase BioDPRO_0000187971Add
    BLAST

    Proteomic databases

    PRIDEiO24872.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    MINTiMINT-8303355.
    STRINGi85962.HP0029.

    Structurei

    Secondary structure

    218
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi1 – 88
    Helixi13 – 2614
    Beta strandi31 – 344
    Beta strandi37 – 404
    Turni43 – 453
    Helixi50 – 5910
    Helixi67 – 704
    Beta strandi76 – 794
    Helixi81 – 888
    Helixi96 – 10510
    Helixi106 – 1083
    Beta strandi111 – 1166
    Beta strandi118 – 1203
    Beta strandi124 – 1285
    Helixi131 – 1388
    Beta strandi141 – 1466
    Helixi152 – 16413
    Beta strandi166 – 1683
    Beta strandi170 – 1745
    Helixi182 – 1865
    Helixi188 – 19710
    Helixi205 – 2073
    Helixi209 – 2179

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2QMOX-ray1.47A1-218[»]
    3MLEX-ray2.80A/B/C/D/E/F1-218[»]
    3QXCX-ray1.34A1-218[»]
    3QXHX-ray1.36A1-218[»]
    3QXJX-ray1.38A1-218[»]
    3QXSX-ray1.35A1-218[»]
    3QXXX-ray1.36A1-218[»]
    3QY0X-ray1.60A1-218[»]
    ProteinModelPortaliO24872.
    SMRiO24872. Positions 1-218.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO24872.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the dethiobiotin synthetase family.Curated

    Phylogenomic databases

    eggNOGiCOG0132.
    KOiK01935.
    OMAiEENMLDF.
    OrthoDBiEOG66B3XT.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00336. BioD.
    InterProiIPR004472. DTB_synth_BioD.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PIRSFiPIRSF006755. DTB_synth. 1 hit.
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00347. bioD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O24872-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLFISATNTN AGKTTCARLL AQYCNACGVK TILLKPIETG VNDAINHSSD    50
    AHLFLQDNRL LDRSLTLKDI SFYRYHKVSA PLIAQQEEDP NAPIDTDNLT 100
    QRLHNFTKTY DLVIVEGAGG LCVPITLEEN MLDFALKLKA KMLLISHDNL 150
    GLINDCLLND FLLKSHQLDY KIAINLKGNN TAFHSISLPY IELFNTRSNN 200
    PIVIFQQSLK VLMSFALK 218
    Length:218
    Mass (Da):24,407
    Last modified:January 1, 1998 - v1
    Checksum:iC818F3D3A88C6015
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000511 Genomic DNA. Translation: AAD07100.1.
    PIRiE64523.
    RefSeqiNP_206831.1. NC_000915.1.
    YP_006933951.1. NC_018939.1.

    Genome annotation databases

    EnsemblBacteriaiAAD07100; AAD07100; HP_0029.
    GeneIDi13869205.
    899125.
    KEGGiheo:C694_00135.
    hpy:HP0029.
    PATRICi20591257. VBIHelPyl33062_0030.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000511 Genomic DNA. Translation: AAD07100.1 .
    PIRi E64523.
    RefSeqi NP_206831.1. NC_000915.1.
    YP_006933951.1. NC_018939.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2QMO X-ray 1.47 A 1-218 [» ]
    3MLE X-ray 2.80 A/B/C/D/E/F 1-218 [» ]
    3QXC X-ray 1.34 A 1-218 [» ]
    3QXH X-ray 1.36 A 1-218 [» ]
    3QXJ X-ray 1.38 A 1-218 [» ]
    3QXS X-ray 1.35 A 1-218 [» ]
    3QXX X-ray 1.36 A 1-218 [» ]
    3QY0 X-ray 1.60 A 1-218 [» ]
    ProteinModelPortali O24872.
    SMRi O24872. Positions 1-218.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    MINTi MINT-8303355.
    STRINGi 85962.HP0029.

    Proteomic databases

    PRIDEi O24872.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD07100 ; AAD07100 ; HP_0029 .
    GeneIDi 13869205.
    899125.
    KEGGi heo:C694_00135.
    hpy:HP0029.
    PATRICi 20591257. VBIHelPyl33062_0030.

    Phylogenomic databases

    eggNOGi COG0132.
    KOi K01935.
    OMAi EENMLDF.
    OrthoDBi EOG66B3XT.

    Enzyme and pathway databases

    UniPathwayi UPA00078 ; UER00161 .
    BioCyci HPY:HP0029-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O24872.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    HAMAPi MF_00336. BioD.
    InterProi IPR004472. DTB_synth_BioD.
    IPR027417. P-loop_NTPase.
    [Graphical view ]
    PIRSFi PIRSF006755. DTB_synth. 1 hit.
    SUPFAMi SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR00347. bioD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700392 / 26695.
    2. "Crystal structure of dethiobiotin synthetase (biod) from Helicobacter pylori."
      Midwest center for structural genomics (MCSG)
      Submitted (MAR-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS).
    3. "Crystal structure of dethiobiotin synthetase (biod) from Helicobacter pylori cocrystallized with ATP."
      Midwest center for structural genomics (MCSG)
      Submitted (MAY-2010) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, SUBUNIT.

    Entry informationi

    Entry nameiBIOD_HELPY
    AccessioniPrimary (citable) accession number: O24872
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 90 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. Helicobacter pylori
      Helicobacter pylori (strain 26695): 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