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P12995 (BIOA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 137. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:bioA
Ordered Locus Names:b0774, JW0757
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length429 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5

Catalytic activity

S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate. HAMAP-Rule MF_00834

Cofactor

Pyridoxal phosphate. Ref.5

Enzyme regulation

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. Ref.6 Ref.8 Ref.12

Pathway

Cofactor biosynthesis; biotin biosynthesis; 7,8-diaminononanoate from 8-amino-7-oxononanoate (SAM route): step 1/1. HAMAP-Rule MF_00834

Subunit structure

Homodimer. Ref.5

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00834.

Induction

Repressed by BirA. Ref.6 Ref.7 Ref.8 Ref.12

Miscellaneous

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

Sequence similarities

Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. BioA subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=1.2 µM for KAPA Ref.6 Ref.11

KM=150 µM for SAM

KM=21 µM for pyridoxamine phosphate (PMP)

KM=32 µM for pyridoxal phosphate (PLP)

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

Ontologies

Keywords
   Biological processBiotin biosynthesis
   Cellular componentCytoplasm
   LigandPyridoxal phosphate
S-adenosyl-L-methionine
   Molecular functionAminotransferase
Transferase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processbiotin biosynthetic process

Inferred from direct assay Ref.5. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionadenosylmethionine-8-amino-7-oxononanoate transaminase activity

Inferred from direct assay Ref.5. Source: UniProtKB

pyridoxal phosphate binding

Inferred from direct assay Ref.5. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 429429Adenosylmethionine-8-amino-7-oxononanoate aminotransferase HAMAP-Rule MF_00834
PRO_0000120366

Regions

Region112 – 1132Pyridoxal phosphate binding HAMAP-Rule MF_00834
Region308 – 3092Pyridoxal phosphate binding HAMAP-Rule MF_00834

Sites

Binding site521Substrate
Binding site1441Substrate Probable
Binding site2451Pyridoxal phosphate
Binding site2741Substrate
Binding site3071Substrate; via carbonyl oxygen
Binding site3911Substrate
Site171Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM Probable

Amino acid modifications

Modified residue2741N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_00834

Experimental info

Mutagenesis171Y → F: Severely reduces the aminotransferase activity. Ref.13
Mutagenesis1441Y → F: Severely reduces the aminotransferase activity. Ref.13
Mutagenesis1471D → N: Loss of aminotransferase activity. Ref.13
Mutagenesis2531R → A: Has only a small effect on the rate of reaction with DAPA. Ref.13
Mutagenesis2531R → K: Increases aminotransferase activity toward SAM. Ref.13
Mutagenesis2531R → M: Loss of aminotransferase activity. Ref.13
Mutagenesis2531R → Q: Increases aminotransferase activity toward SAM. Ref.13
Mutagenesis3911R → A: Reduces aminotransferase activity. Ref.11
Sequence conflict111R → P in CAA00964. Ref.2
Sequence conflict99 – 1024TPQP → SGRNA in AAA23514. Ref.1

Secondary structure

................................................................................... 429
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P12995 [UniParc].

Last modified October 1, 1994. Version 2.
Checksum: 84D2D1AE3A1280FF

FASTA42947,336
        10         20         30         40         50         60 
MTTDDLAFDQ RHIWHPYTSM TSPLPVYPVV SAEGCELILS DGRRLVDGMS SWWAAIHGYN 

        70         80         90        100        110        120 
HPQLNAAMKS QIDAMSHVMF GGITHAPAIE LCRKLVAMTP QPLECVFLAD SGSVAVEVAM 

       130        140        150        160        170        180 
KMALQYWQAK GEARQRFLTF RNGYHGDTFG AMSVCDPDNS MHSLWKGYLP ENLFAPAPQS 

       190        200        210        220        230        240 
RMDGEWDERD MVGFARLMAA HRHEIAAVII EPIVQGAGGM RMYHPEWLKR IRKICDREGI 

       250        260        270        280        290        300 
LLIADEIATG FGRTGKLFAC EHAEIAPDIL CLGKALTGGT MTLSATLTTR EVAETISNGE 

       310        320        330        340        350        360 
AGCFMHGPTF MGNPLACAAA NASLAILESG DWQQQVADIE VQLREQLAPA RDAEMVADVR 

       370        380        390        400        410        420 
VLGAIGVVET THPVNMAALQ KFFVEQGVWI RPFGKLIYLM PPYIILPQQL QRLTAAVNRA 


VQDETFFCQ 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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 ANALOGS SUBSTRATE, 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J04423 Genomic DNA. Translation: AAA23514.1.
A11524 Unassigned DNA. Translation: CAA00964.1.
U00096 Genomic DNA. Translation: AAC73861.1.
AP009048 Genomic DNA. Translation: BAE76361.1.
PIRXNECDP. F64813.
RefSeqNP_415295.1. NC_000913.3.
YP_489047.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP12995.
SMRP12995. Positions 1-429.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9219N.
IntActP12995. 5 interactions.
MINTMINT-1275136.
STRING511145.b0774.

Proteomic databases

PaxDbP12995.
PRIDEP12995.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73861; AAC73861; b0774.
BAE76361; BAE76361; BAE76361.
GeneID12932847.
945376.
KEGGecj:Y75_p0747.
eco:b0774.
PATRIC32116749. VBIEscCol129921_0800.

Organism-specific databases

EchoBASEEB0115.
EcoGeneEG10117. bioA.

Phylogenomic databases

eggNOGCOG0161.
HOGENOMHOG000020209.
KOK00833.
OMAREACDRY.
OrthoDBEOG6QVRHN.
PhylomeDBP12995.
ProtClustDBPRK07986.

Enzyme and pathway databases

BioCycEcoCyc:DAPASYN-MONOMER.
ECOL316407:JW0757-MONOMER.
MetaCyc:DAPASYN-MONOMER.
BRENDA2.6.1.62. 2026.
SABIO-RKP12995.
UniPathwayUPA00078; UER00160.

Gene expression databases

GenevestigatorP12995.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 2 hits.
HAMAPMF_00834. BioA.
InterProIPR005814. Aminotrans_3.
IPR005815. BioA.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERPTHR11986. PTHR11986. 1 hit.
PTHR11986:SF8. PTHR11986:SF8. 1 hit.
PfamPF00202. Aminotran_3. 1 hit.
[Graphical view]
PIRSFPIRSF000521. Transaminase_4ab_Lys_Orn. 1 hit.
SUPFAMSSF53383. SSF53383. 1 hit.
TIGRFAMsTIGR00508. bioA. 1 hit.
PROSITEPS00600. AA_TRANSFER_CLASS_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP12995.
PROP12995.

Entry information

Entry nameBIOA_ECOLI
AccessionPrimary (citable) accession number: P12995
Secondary accession number(s): Q2MBJ5
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: October 1, 1994
Last modified: April 16, 2014
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene