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P12995

- BIOA_ECOLI

UniProt

P12995 - BIOA_ECOLI

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Protein

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Gene
bioA, b0774, JW0757
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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.UniRule annotation

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 SAM
  3. KM=21 µM for pyridoxamine phosphate (PMP)
  4. KM=32 µM for pyridoxal phosphate (PLP)
  5. KM=1000 µM for 8-keto-7-aminopelargonic acid

Vmax=0.16 µmol/min/mg enzyme with KAPA as substrate

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

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 SAM Inferred
Binding sitei52 – 521Substrate
Binding sitei144 – 1441Substrate Inferred
Binding sitei245 – 2451Pyridoxal phosphate
Binding sitei274 – 2741Substrate
Binding sitei307 – 3071Substrate; via carbonyl oxygen
Binding sitei391 – 3911Substrate

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
Complete GO annotation...

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 UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

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 aminotransferaseUniRule annotationPRO_0000120366Add
BLAST

Amino acid modifications

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

Proteomic databases

PaxDbiP12995.
PRIDEiP12995.

Expressioni

Inductioni

Repressed by BirA.4 Publications

Gene expression databases

GenevestigatoriP12995.

Interactioni

Subunit structurei

Homodimer.1 Publication

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.

Miscellaneous databases

EvolutionaryTraceiP12995.

Family & Domainsi

Region

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

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

Sequence conflict

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

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 140 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

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