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P12995

- BIOA_ECOLI

UniProt

P12995 - BIOA_ECOLI

Protein

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Gene

bioA

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 141 (01 Oct 2014)
      Sequence version 2 (01 Oct 1994)
      Previous versions | rss
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    Functioni

    Catalyzes the transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor.1 Publication

    Catalytic activityi

    S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate.

    Cofactori

    Pyridoxal phosphate.1 Publication

    Enzyme regulationi

    Inhibited by amiclenomycin. S-adenosyl-L-(2-hydroxy-4-methylthio)butyric acid and adenosine are competitive inhibitors with SAM and uncompetitive inhibitors with KAPA as substrates. S-adenosyl-L-ethionine, adenine and 8-keto-7-aminopelargonic acid are non-competitive inhibitors with both substrates.3 Publications

    Kineticsi

    1. KM=1.2 µM for KAPA2 Publications
    2. KM=150 µM for SAM2 Publications
    3. KM=21 µM for pyridoxamine phosphate (PMP)2 Publications
    4. KM=32 µM for pyridoxal phosphate (PLP)2 Publications
    5. KM=1000 µM for 8-keto-7-aminopelargonic acid2 Publications

    Vmax=0.16 µmol/min/mg enzyme with KAPA as substrate2 Publications

    Vmax=0.027 µmol/min/mg enzyme with 8-keto-7-aminopelargonic acid as substrate2 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei17 – 171Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAMCurated
    Binding sitei52 – 521Substrate1 Publication
    Binding sitei144 – 1441Substrate1 Publication
    Binding sitei245 – 2451Pyridoxal phosphate3 Publications
    Binding sitei274 – 2741Substrate1 Publication
    Binding sitei307 – 3071Substrate; via carbonyl oxygen1 Publication
    Binding sitei391 – 3911Substrate1 Publication

    GO - Molecular functioni

    1. adenosylmethionine-8-amino-7-oxononanoate transaminase activity Source: UniProtKB
    2. pyridoxal phosphate binding Source: UniProtKB

    GO - Biological processi

    1. biotin biosynthetic process Source: UniProtKB

    Keywords - Molecular functioni

    Aminotransferase, Transferase

    Keywords - Biological processi

    Biotin biosynthesis

    Keywords - Ligandi

    Pyridoxal phosphate, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciEcoCyc:DAPASYN-MONOMER.
    ECOL316407:JW0757-MONOMER.
    MetaCyc:DAPASYN-MONOMER.
    BRENDAi2.6.1.62. 2026.
    SABIO-RKP12995.
    UniPathwayiUPA00078; UER00160.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC:2.6.1.62)
    Alternative name(s):
    7,8-diamino-pelargonic acid aminotransferase
    Short name:
    DAPA AT
    Short name:
    DAPA aminotransferase
    7,8-diaminononanoate synthase
    Short name:
    DANS
    Diaminopelargonic acid synthase
    Gene namesi
    Name:bioA
    Ordered Locus Names:b0774, JW0757
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10117. bioA.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi17 – 171Y → F: Severely reduces the aminotransferase activity. 1 Publication
    Mutagenesisi144 – 1441Y → F: Severely reduces the aminotransferase activity. 1 Publication
    Mutagenesisi147 – 1471D → N: Loss of aminotransferase activity. 1 Publication
    Mutagenesisi253 – 2531R → A: Has only a small effect on the rate of reaction with DAPA. 1 Publication
    Mutagenesisi253 – 2531R → K: Increases aminotransferase activity toward SAM. 1 Publication
    Mutagenesisi253 – 2531R → M: Loss of aminotransferase activity. 1 Publication
    Mutagenesisi253 – 2531R → Q: Increases aminotransferase activity toward SAM. 1 Publication
    Mutagenesisi391 – 3911R → A: Reduces aminotransferase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 429429Adenosylmethionine-8-amino-7-oxononanoate aminotransferasePRO_0000120366Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei274 – 2741N6-(pyridoxal phosphate)lysine

    Proteomic databases

    PaxDbiP12995.
    PRIDEiP12995.

    Expressioni

    Inductioni

    Repressed by BirA.1 Publication

    Gene expression databases

    GenevestigatoriP12995.

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    Protein-protein interaction databases

    DIPiDIP-9219N.
    IntActiP12995. 5 interactions.
    MINTiMINT-1275136.
    STRINGi511145.b0774.

    Structurei

    Secondary structure

    1
    429
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1210
    Beta strandi20 – 223
    Beta strandi27 – 348
    Beta strandi36 – 394
    Beta strandi44 – 496
    Turni50 – 545
    Helixi62 – 7413
    Beta strandi81 – 844
    Helixi86 – 9813
    Beta strandi105 – 1117
    Helixi112 – 13019
    Beta strandi136 – 1405
    Helixi149 – 1524
    Turni157 – 1615
    Helixi162 – 1654
    Turni166 – 1683
    Beta strandi173 – 1753
    Beta strandi180 – 1845
    Helixi188 – 1914
    Helixi192 – 20110
    Turni202 – 2043
    Beta strandi205 – 2106
    Beta strandi212 – 2154
    Turni217 – 2193
    Beta strandi221 – 2233
    Helixi226 – 23813
    Beta strandi241 – 2455
    Turni247 – 2548
    Beta strandi255 – 2584
    Helixi259 – 2635
    Beta strandi268 – 2725
    Helixi274 – 2774
    Beta strandi279 – 2813
    Beta strandi284 – 2885
    Helixi290 – 2978
    Beta strandi299 – 3035
    Turni309 – 3124
    Helixi314 – 32815
    Helixi332 – 34716
    Helixi348 – 3525
    Beta strandi356 – 3627
    Beta strandi365 – 3728
    Helixi376 – 38510
    Beta strandi396 – 3994
    Helixi407 – 42014
    Helixi424 – 4263

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DTYX-ray2.14A/B1-429[»]
    1MGVX-ray2.10A/B1-429[»]
    1MLYX-ray1.81A/B1-429[»]
    1MLZX-ray2.15A/B1-429[»]
    1QJ3X-ray2.70A/B1-429[»]
    1QJ5X-ray1.80A/B1-429[»]
    1S06X-ray2.20A/B1-429[»]
    1S07X-ray2.42A/B1-429[»]
    1S08X-ray2.10A/B1-429[»]
    1S09X-ray1.83A/B1-429[»]
    1S0AX-ray1.71A/B1-429[»]
    ProteinModelPortaliP12995.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12995.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni112 – 1132Pyridoxal phosphate binding
    Regioni308 – 3092Pyridoxal phosphate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0161.
    HOGENOMiHOG000020209.
    KOiK00833.
    OMAiPWQERRG.
    OrthoDBiEOG6QVRHN.
    PhylomeDBiP12995.

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 2 hits.
    HAMAPiMF_00834. BioA.
    InterProiIPR005814. Aminotrans_3.
    IPR005815. BioA.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PANTHERiPTHR11986. PTHR11986. 1 hit.
    PfamiPF00202. Aminotran_3. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000521. Transaminase_4ab_Lys_Orn. 1 hit.
    SUPFAMiSSF53383. SSF53383. 1 hit.
    TIGRFAMsiTIGR00508. bioA. 1 hit.
    PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P12995-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTTDDLAFDQ RHIWHPYTSM TSPLPVYPVV SAEGCELILS DGRRLVDGMS    50
    SWWAAIHGYN HPQLNAAMKS QIDAMSHVMF GGITHAPAIE LCRKLVAMTP 100
    QPLECVFLAD SGSVAVEVAM KMALQYWQAK GEARQRFLTF RNGYHGDTFG 150
    AMSVCDPDNS MHSLWKGYLP ENLFAPAPQS RMDGEWDERD MVGFARLMAA 200
    HRHEIAAVII EPIVQGAGGM RMYHPEWLKR IRKICDREGI LLIADEIATG 250
    FGRTGKLFAC EHAEIAPDIL CLGKALTGGT MTLSATLTTR EVAETISNGE 300
    AGCFMHGPTF MGNPLACAAA NASLAILESG DWQQQVADIE VQLREQLAPA 350
    RDAEMVADVR VLGAIGVVET THPVNMAALQ KFFVEQGVWI RPFGKLIYLM 400
    PPYIILPQQL QRLTAAVNRA VQDETFFCQ 429
    Length:429
    Mass (Da):47,336
    Last modified:October 1, 1994 - v2
    Checksum:i84D2D1AE3A1280FF
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti11 – 111R → P in CAA00964. 1 PublicationCurated
    Sequence conflicti99 – 1024TPQP → SGRNA in AAA23514. (PubMed:3058702)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J04423 Genomic DNA. Translation: AAA23514.1.
    A11524 Unassigned DNA. Translation: CAA00964.1.
    U00096 Genomic DNA. Translation: AAC73861.1.
    AP009048 Genomic DNA. Translation: BAE76361.1.
    PIRiF64813. XNECDP.
    RefSeqiNP_415295.1. NC_000913.3.
    YP_489047.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73861; AAC73861; b0774.
    BAE76361; BAE76361; BAE76361.
    GeneIDi12932847.
    945376.
    KEGGiecj:Y75_p0747.
    eco:b0774.
    PATRICi32116749. VBIEscCol129921_0800.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J04423 Genomic DNA. Translation: AAA23514.1 .
    A11524 Unassigned DNA. Translation: CAA00964.1 .
    U00096 Genomic DNA. Translation: AAC73861.1 .
    AP009048 Genomic DNA. Translation: BAE76361.1 .
    PIRi F64813. XNECDP.
    RefSeqi NP_415295.1. NC_000913.3.
    YP_489047.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DTY X-ray 2.14 A/B 1-429 [» ]
    1MGV X-ray 2.10 A/B 1-429 [» ]
    1MLY X-ray 1.81 A/B 1-429 [» ]
    1MLZ X-ray 2.15 A/B 1-429 [» ]
    1QJ3 X-ray 2.70 A/B 1-429 [» ]
    1QJ5 X-ray 1.80 A/B 1-429 [» ]
    1S06 X-ray 2.20 A/B 1-429 [» ]
    1S07 X-ray 2.42 A/B 1-429 [» ]
    1S08 X-ray 2.10 A/B 1-429 [» ]
    1S09 X-ray 1.83 A/B 1-429 [» ]
    1S0A X-ray 1.71 A/B 1-429 [» ]
    ProteinModelPortali P12995.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9219N.
    IntActi P12995. 5 interactions.
    MINTi MINT-1275136.
    STRINGi 511145.b0774.

    Proteomic databases

    PaxDbi P12995.
    PRIDEi P12995.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73861 ; AAC73861 ; b0774 .
    BAE76361 ; BAE76361 ; BAE76361 .
    GeneIDi 12932847.
    945376.
    KEGGi ecj:Y75_p0747.
    eco:b0774.
    PATRICi 32116749. VBIEscCol129921_0800.

    Organism-specific databases

    EchoBASEi EB0115.
    EcoGenei EG10117. bioA.

    Phylogenomic databases

    eggNOGi COG0161.
    HOGENOMi HOG000020209.
    KOi K00833.
    OMAi PWQERRG.
    OrthoDBi EOG6QVRHN.
    PhylomeDBi P12995.

    Enzyme and pathway databases

    UniPathwayi UPA00078 ; UER00160 .
    BioCyci EcoCyc:DAPASYN-MONOMER.
    ECOL316407:JW0757-MONOMER.
    MetaCyc:DAPASYN-MONOMER.
    BRENDAi 2.6.1.62. 2026.
    SABIO-RK P12995.

    Miscellaneous databases

    EvolutionaryTracei P12995.
    PROi P12995.

    Gene expression databases

    Genevestigatori P12995.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    3.90.1150.10. 2 hits.
    HAMAPi MF_00834. BioA.
    InterProi IPR005814. Aminotrans_3.
    IPR005815. BioA.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view ]
    PANTHERi PTHR11986. PTHR11986. 1 hit.
    Pfami PF00202. Aminotran_3. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000521. Transaminase_4ab_Lys_Orn. 1 hit.
    SUPFAMi SSF53383. SSF53383. 1 hit.
    TIGRFAMsi TIGR00508. bioA. 1 hit.
    PROSITEi PS00600. AA_TRANSFER_CLASS_3. 1 hit.
    [Graphical view ]
    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. "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].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "Purification and properties of 7, 8-diaminopelargonic acid aminotransferase. An enzyme in the biotin biosynthetic pathway."
      Stoner G.L., Eisenberg M.A.
      J. Biol. Chem. 250:4029-4036(1975) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS AN AMINOTRANSFERASE, SUBUNIT, SUBSTRATE SPECIFICITY, COFACTOR.
    6. "Biosynthesis of 7, 8-diaminopelargonic acid from 7-keto-8-aminopelargonic acid and S-adenosyl-L-methionine. The kinetics of the reaction."
      Stoner G.L., Eisenberg M.A.
      J. Biol. Chem. 250:4037-4043(1975) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, ENZYME REGULATION.
    7. "Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli."
      Barker D.F., Campbell A.M.
      J. Mol. Biol. 146:469-492(1981) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    8. "Inhibition of 7,8-diaminopelargonic acid aminotransferase by amiclenomycin and analogues."
      Mann S., Marquet A., Ploux O.
      Biochem. Soc. Trans. 33:802-805(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION.
    9. "Biotin synthesis begins by hijacking the fatty acid synthetic pathway."
      Lin S., Hanson R.E., Cronan J.E.
      Nat. Chem. Biol. 6:682-688(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBSTRATE SPECIFICITY.
    10. "Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes."
      Kaeck H., Sandmark J., Gibson K., Schneider G., Lindqvist Y.
      J. Mol. Biol. 291:857-876(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND PYRIDOXAL PHOSPHATE.
      Strain: B / BL21-DE3.
    11. "The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation."
      Eliot A.C., Sandmark J., Schneider G., Kirsch J.F.
      Biochemistry 41:12582-12589(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND MUTANTS ALA-391, MUTAGENESIS OF ARG-391, BIOPHYSICOCHEMICAL PROPERTIES.
    12. "Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin."
      Sandmark J., Mann S., Marquet A., Schneider G.
      J. Biol. Chem. 277:43352-43358(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ENZYME REGULATION.
    13. "Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis."
      Sandmark J., Eliot A.C., Famm K., Schneider G., Kirsch J.F.
      Biochemistry 43:1213-1222(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANTS PHE-17; PHE-144; ASN-147; ALA-253 AND LYS-253 IN COMPLEX WITH PYRIDOXAL PHOSPHATE, MUTAGENESIS OF TYR-17; TYR-144; ASP-147 AND ARG-253.

    Entry informationi

    Entry nameiBIOA_ECOLI
    AccessioniPrimary (citable) accession number: P12995
    Secondary accession number(s): Q2MBJ5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 141 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Catalysis proceeds by a classical ping-pong bi-bi reaction mechanism.

    Keywords - Technical termi

    3D-structure, Complete proteome, 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