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P12998

- BIOF_ECOLI

UniProt

P12998 - BIOF_ECOLI

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Protein
8-amino-7-oxononanoate synthase
Gene
bioF, b0776, JW0759
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. Can also use pimeloyl-CoA instead of pimeloyl-ACP as substrate, but it is believed that pimeloyl-ACP rather than pimeloyl-CoA is the physiological substrate of BioF.1 Publication

Catalytic activityi

Pimeloyl-[acyl-carrier protein] + L-alanine = 8-amino-7-oxononanoate + CO2 + holo-[acyl-carrier protein].1 Publication

Cofactori

Pyridoxal phosphate.1 Publication

Enzyme regulationi

Competitively inhibited by D-alanine, 8-amino-7-hydroxy-8-phosphonononanoic acid and 2-amino-3-hydroxy-2-methylnonadioic acid.1 Publication

Kineticsi

  1. KM=25 µM for pimeloyl-CoA (at pH 7.5 and at 30 degrees Celsius)1 Publication
  2. KM=0.5 µM for L-alanine (at pH 7.5 and at 30 degrees Celsius)

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei21 – 211Substrate
Binding sitei133 – 1331Substrate
Binding sitei179 – 1791Pyridoxal phosphate
Binding sitei352 – 3521Substrate

GO - Molecular functioni

  1. 8-amino-7-oxononanoate synthase activity Source: EcoCyc
  2. pyridoxal phosphate binding Source: UniProtKB

GO - Biological processi

  1. biotin biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Biotin biosynthesis

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:7KAPSYN-MONOMER.
ECOL316407:JW0759-MONOMER.
MetaCyc:7KAPSYN-MONOMER.
UniPathwayiUPA00078.

Names & Taxonomyi

Protein namesi
Recommended name:
8-amino-7-oxononanoate synthase (EC:2.3.1.47)
Short name:
AONS
Alternative name(s):
7-keto-8-amino-pelargonic acid synthase
Short name:
7-KAP synthase
Short name:
KAPA synthase
8-amino-7-ketopelargonate synthase
Gene namesi
Name:bioF
Ordered Locus Names:b0776, JW0759
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10121. bioF.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 3843838-amino-7-oxononanoate synthaseUniRule annotation
PRO_0000163811Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei236 – 2361N6-(pyridoxal phosphate)lysineUniRule annotation

Proteomic databases

PaxDbiP12998.
PRIDEiP12998.

Expressioni

Gene expression databases

GenevestigatoriP12998.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

DIPiDIP-6870N.
IntActiP12998. 2 interactions.
STRINGi511145.b0776.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1311
Helixi16 – 183
Beta strandi30 – 367
Beta strandi39 – 435
Helixi52 – 543
Helixi56 – 6914
Turni77 – 804
Helixi84 – 9714
Beta strandi100 – 1067
Helixi108 – 11912
Beta strandi125 – 1295
Helixi134 – 1418
Beta strandi143 – 1508
Helixi155 – 1639
Beta strandi170 – 1778
Turni179 – 1813
Helixi187 – 19610
Beta strandi200 – 2045
Turni206 – 2116
Helixi214 – 2163
Helixi219 – 2224
Beta strandi228 – 2369
Beta strandi243 – 2475
Helixi249 – 25810
Helixi260 – 2634
Beta strandi264 – 2663
Helixi270 – 28415
Helixi286 – 30621
Beta strandi309 – 3113
Beta strandi318 – 3203
Beta strandi323 – 3275
Helixi328 – 34013
Turni350 – 3523
Beta strandi358 – 3603
Helixi370 – 38314

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BS0X-ray1.65A1-384[»]
1DJ9X-ray2.00A1-384[»]
1DJEX-ray1.71A1-384[»]
2G6WX-ray2.14A1-384[»]
ProteinModelPortaliP12998.
SMRiP12998. Positions 2-384.

Miscellaneous databases

EvolutionaryTraceiP12998.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni108 – 1092Pyridoxal phosphate bindingUniRule annotation
Regioni204 – 2074Pyridoxal phosphate bindingUniRule annotation
Regioni233 – 2364Pyridoxal phosphate bindingUniRule annotation

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0156.
HOGENOMiHOG000221021.
KOiK00652.
OMAiRICLHAF.
OrthoDBiEOG6Q8HZD.
PhylomeDBiP12998.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_01693. BioF_aminotrans_2.
InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR004723. AONS_Archaea/Proteobacteria.
IPR022834. AONS_Proteobacteria.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR00858. bioF. 1 hit.
PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P12998-1 [UniParc]FASTAAdd to Basket

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MSWQEKINAA LDARRAADAL RRRYPVAQGA GRWLVADDRQ YLNFSSNDYL    50
GLSHHPQIIR AWQQGAEQFG IGSGGSGHVS GYSVVHQALE EELAEWLGYS 100
RALLFISGFA ANQAVIAAMM AKEDRIAADR LSHASLLEAA SLSPSQLRRF 150
AHNDVTHLAR LLASPCPGQQ MVVTEGVFSM DGDSAPLAEI QQVTQQHNGW 200
LMVDDAHGTG VIGEQGRGSC WLQKVKPELL VVTFGKGFGV SGAAVLCSST 250
VADYLLQFAR HLIYSTSMPP AQAQALRASL AVIRSDEGDA RREKLAALIT 300
RFRAGVQDLP FTLADSCSAI QPLIVGDNSR ALQLAEKLRQ QGCWVTAIRP 350
PTVPAGTARL RLTLTAAHEM QDIDRLLEVL HGNG 384
Length:384
Mass (Da):41,594
Last modified:January 1, 1990 - v1
Checksum:iD1AF5C054A5B4B06
GO

Mass spectrometryi

Molecular mass is 41464.4±4.5 Da from positions 2 - 384. Determined by ESI. 1 Publication

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti188 – 1892AE → R in CAA00968. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J04423 Genomic DNA. Translation: AAA23516.1.
A11542 Unassigned DNA. Translation: CAA00968.1.
U00096 Genomic DNA. Translation: AAC73863.1.
AP009048 Genomic DNA. Translation: BAE76363.1.
PIRiD32025. SYECKP.
RefSeqiNP_415297.1. NC_000913.3.
YP_489049.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73863; AAC73863; b0776.
BAE76363; BAE76363; BAE76363.
GeneIDi12930959.
945384.
KEGGiecj:Y75_p0749.
eco:b0776.
PATRICi32116753. VBIEscCol129921_0802.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J04423 Genomic DNA. Translation: AAA23516.1 .
A11542 Unassigned DNA. Translation: CAA00968.1 .
U00096 Genomic DNA. Translation: AAC73863.1 .
AP009048 Genomic DNA. Translation: BAE76363.1 .
PIRi D32025. SYECKP.
RefSeqi NP_415297.1. NC_000913.3.
YP_489049.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1BS0 X-ray 1.65 A 1-384 [» ]
1DJ9 X-ray 2.00 A 1-384 [» ]
1DJE X-ray 1.71 A 1-384 [» ]
2G6W X-ray 2.14 A 1-384 [» ]
ProteinModelPortali P12998.
SMRi P12998. Positions 2-384.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6870N.
IntActi P12998. 2 interactions.
STRINGi 511145.b0776.

Proteomic databases

PaxDbi P12998.
PRIDEi P12998.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73863 ; AAC73863 ; b0776 .
BAE76363 ; BAE76363 ; BAE76363 .
GeneIDi 12930959.
945384.
KEGGi ecj:Y75_p0749.
eco:b0776.
PATRICi 32116753. VBIEscCol129921_0802.

Organism-specific databases

EchoBASEi EB0119.
EcoGenei EG10121. bioF.

Phylogenomic databases

eggNOGi COG0156.
HOGENOMi HOG000221021.
KOi K00652.
OMAi RICLHAF.
OrthoDBi EOG6Q8HZD.
PhylomeDBi P12998.

Enzyme and pathway databases

UniPathwayi UPA00078 .
BioCyci EcoCyc:7KAPSYN-MONOMER.
ECOL316407:JW0759-MONOMER.
MetaCyc:7KAPSYN-MONOMER.

Miscellaneous databases

EvolutionaryTracei P12998.
PROi P12998.

Gene expression databases

Genevestigatori P12998.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPi MF_01693. BioF_aminotrans_2.
InterProi IPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR004723. AONS_Archaea/Proteobacteria.
IPR022834. AONS_Proteobacteria.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view ]
Pfami PF00155. Aminotran_1_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
TIGRFAMsi TIGR00858. bioF. 1 hit.
PROSITEi PS00599. AA_TRANSFER_CLASS_2. 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. "Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies."
    Webster S.P., Alexeev D., Campopiano D.J., Watt R.M., Alexeeva M., Sawyer L., Baxter R.L.
    Biochemistry 39:516-528(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-6, X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND SUBSTRATE, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MASS SPECTROMETRY, REACTION MECHANISM.
  6. "Slow-binding and competitive inhibition of 8-amino-7-oxopelargonate synthase, a pyridoxal-5'-phosphate-dependent enzyme involved in biotin biosynthesis, by substrate and intermediate analogs. Kinetic and binding studies."
    Ploux O., Breyne O., Carillon S., Marquet A.
    Eur. J. Biochem. 259:63-70(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  7. "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: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
  8. "The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme."
    Alexeev D., Alexeeva M., Baxter R.L., Campopiano D.J., Webster S.P., Sawyer L.
    J. Mol. Biol. 284:401-419(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), SUBUNIT.
  9. "Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine."
    Alexeev D., Baxter R.L., Campopiano D.J., Kerbarh O., Sawyer L., Tomczyk N., Watt R., Webster S.P.
    Org. Biomol. Chem. 4:1209-1212(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.14 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.

Entry informationi

Entry nameiBIOF_ECOLI
AccessioniPrimary (citable) accession number: P12998
Secondary accession number(s): Q2MBJ3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: September 3, 2014
This is version 130 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, 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

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