BIOF_ECOLI
ID BIOF_ECOLI Reviewed; 384 AA.
AC P12998; Q2MBJ3;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1990, sequence version 1.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=8-amino-7-oxononanoate synthase {ECO:0000303|PubMed:10642176};
DE Short=AONS {ECO:0000303|PubMed:10642176};
DE EC=2.3.1.47 {ECO:0000269|PubMed:10642176, ECO:0000269|PubMed:20693992};
DE AltName: Full=7-keto-8-amino-pelargonic acid synthase {ECO:0000303|PubMed:3058702};
DE Short=7-KAP synthase {ECO:0000303|PubMed:3058702};
DE Short=KAPA synthase {ECO:0000303|PubMed:3058702};
DE AltName: Full=8-amino-7-ketopelargonate synthase;
GN Name=bioF {ECO:0000303|PubMed:3058702}; OrderedLocusNames=b0776, JW0759;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PATHWAY.
RX PubMed=3058702; DOI=10.1016/s0021-9258(19)77675-3;
RA Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O.,
RA Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.;
RT "The Escherichia coli biotin biosynthetic enzyme sequences predicted from
RT the nucleotide sequence of the bio operon.";
RL J. Biol. Chem. 263:19577-19585(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Pearson B.M., McKee R.A.;
RT "Genetic material for expression of biotin synthetase enzymes.";
RL Patent number GB2216530, 11-OCT-1989.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-6, X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX
RP WITH PYRIDOXAL PHOSPHATE AND SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MASS SPECTROMETRY, SUBUNIT, AND
RP REACTION MECHANISM.
RX PubMed=10642176; DOI=10.1021/bi991620j;
RA Webster S.P., Alexeev D., Campopiano D.J., Watt R.M., Alexeeva M.,
RA Sawyer L., Baxter R.L.;
RT "Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and
RT crystallographic studies.";
RL Biochemistry 39:516-528(2000).
RN [6]
RP ACTIVITY REGULATION.
RX PubMed=9914476; DOI=10.1046/j.1432-1327.1999.00006.x;
RA Ploux O., Breyne O., Carillon S., Marquet A.;
RT "Slow-binding and competitive inhibition of 8-amino-7-oxopelargonate
RT synthase, a pyridoxal-5'-phosphate-dependent enzyme involved in biotin
RT biosynthesis, by substrate and intermediate analogs. Kinetic and binding
RT studies.";
RL Eur. J. Biochem. 259:63-70(1999).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBSTRATE SPECIFICITY.
RX PubMed=20693992; DOI=10.1038/nchembio.420;
RA Lin S., Hanson R.E., Cronan J.E.;
RT "Biotin synthesis begins by hijacking the fatty acid synthetic pathway.";
RL Nat. Chem. Biol. 6:682-688(2010).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), AND SUBUNIT.
RX PubMed=9813126; DOI=10.1006/jmbi.1998.2086;
RA Alexeev D., Alexeeva M., Baxter R.L., Campopiano D.J., Webster S.P.,
RA Sawyer L.;
RT "The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-
RT dependent, acyl-CoA-condensing enzyme.";
RL J. Mol. Biol. 284:401-419(1998).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.14 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP ANALOG, AND SUBUNIT.
RX PubMed=16557306; DOI=10.1039/b517922j;
RA Alexeev D., Baxter R.L., Campopiano D.J., Kerbarh O., Sawyer L.,
RA Tomczyk N., Watt R., Webster S.P.;
RT "Suicide inhibition of alpha-oxamine synthases: structures of the covalent
RT adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine.";
RL Org. Biomol. Chem. 4:1209-1212(2006).
CC -!- FUNCTION: Catalyzes the decarboxylative condensation of pimeloyl-[acyl-
CC carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON),
CC [acyl-carrier protein], and carbon dioxide. Can also use pimeloyl-CoA
CC instead of pimeloyl-ACP as substrate, but it is believed that pimeloyl-
CC ACP rather than pimeloyl-CoA is the physiological substrate of BioF.
CC {ECO:0000269|PubMed:10642176, ECO:0000269|PubMed:20693992}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-
CC oxononanoate + CO2 + holo-[ACP]; Xref=Rhea:RHEA:42288, Rhea:RHEA-
CC COMP:9685, Rhea:RHEA-COMP:9955, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57972, ChEBI:CHEBI:64479, ChEBI:CHEBI:78846,
CC ChEBI:CHEBI:149468; EC=2.3.1.47;
CC Evidence={ECO:0000269|PubMed:10642176, ECO:0000269|PubMed:20693992};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:10642176};
CC -!- ACTIVITY REGULATION: Competitively inhibited by D-alanine, 8-amino-7-
CC hydroxy-8-phosphonononanoic acid and 2-amino-3-hydroxy-2-
CC methylnonadioic acid. {ECO:0000269|PubMed:9914476}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=25 uM for pimeloyl-CoA (at pH 7.5 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:10642176};
CC KM=0.5 uM for L-alanine (at pH 7.5 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:10642176};
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis.
CC {ECO:0000305|PubMed:3058702}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10642176,
CC ECO:0000269|PubMed:16557306, ECO:0000269|PubMed:9813126}.
CC -!- MASS SPECTROMETRY: Mass=41464.4; Mass_error=4.5; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:10642176};
CC -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. BioF subfamily. {ECO:0000305}.
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DR EMBL; J04423; AAA23516.1; -; Genomic_DNA.
DR EMBL; A11542; CAA00968.1; -; Unassigned_DNA.
DR EMBL; U00096; AAC73863.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76363.1; -; Genomic_DNA.
DR PIR; D32025; SYECKP.
DR RefSeq; NP_415297.1; NC_000913.3.
DR RefSeq; WP_000118826.1; NZ_STEB01000028.1.
DR PDB; 1BS0; X-ray; 1.65 A; A=1-384.
DR PDB; 1DJ9; X-ray; 2.00 A; A=1-384.
DR PDB; 1DJE; X-ray; 1.71 A; A=1-384.
DR PDB; 2G6W; X-ray; 2.14 A; A=1-384.
DR PDBsum; 1BS0; -.
DR PDBsum; 1DJ9; -.
DR PDBsum; 1DJE; -.
DR PDBsum; 2G6W; -.
DR AlphaFoldDB; P12998; -.
DR SMR; P12998; -.
DR BioGRID; 4259953; 19.
DR DIP; DIP-6870N; -.
DR IntAct; P12998; 2.
DR STRING; 511145.b0776; -.
DR DrugBank; DB03160; N-Pyridoxyl-7-Keto-8-Aminopelargonic Acid-5'-Monophosphate.
DR PaxDb; P12998; -.
DR PRIDE; P12998; -.
DR EnsemblBacteria; AAC73863; AAC73863; b0776.
DR EnsemblBacteria; BAE76363; BAE76363; BAE76363.
DR GeneID; 945384; -.
DR KEGG; ecj:JW0759; -.
DR KEGG; eco:b0776; -.
DR PATRIC; fig|1411691.4.peg.1502; -.
DR EchoBASE; EB0119; -.
DR eggNOG; COG0156; Bacteria.
DR HOGENOM; CLU_015846_11_2_6; -.
DR InParanoid; P12998; -.
DR OMA; HYHASGI; -.
DR PhylomeDB; P12998; -.
DR BioCyc; EcoCyc:7KAPSYN-MON; -.
DR BioCyc; MetaCyc:7KAPSYN-MON; -.
DR BRENDA; 2.3.1.47; 2026.
DR SABIO-RK; P12998; -.
DR UniPathway; UPA00078; -.
DR EvolutionaryTrace; P12998; -.
DR PRO; PR:P12998; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008710; F:8-amino-7-oxononanoate synthase activity; IDA:EcoCyc.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0009102; P:biotin biosynthetic process; IMP:EcoCyc.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_01693; BioF_aminotrans_2; 1.
DR InterPro; IPR001917; Aminotrans_II_pyridoxalP_BS.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR004723; AONS_Archaea/Proteobacteria.
DR InterPro; IPR022834; AONS_Proteobacteria.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR00858; bioF; 1.
DR PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Biotin biosynthesis; Direct protein sequencing;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10642176"
FT CHAIN 2..384
FT /note="8-amino-7-oxononanoate synthase"
FT /id="PRO_0000163811"
FT BINDING 21
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10642176"
FT BINDING 108..109
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:10642176,
FT ECO:0000269|PubMed:16557306"
FT BINDING 133
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10642176"
FT BINDING 179
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:10642176,
FT ECO:0000269|PubMed:16557306"
FT BINDING 207
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:10642176,
FT ECO:0000269|PubMed:16557306"
FT BINDING 233
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:10642176"
FT BINDING 352
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10642176"
FT MOD_RES 236
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:10642176,
FT ECO:0000269|PubMed:16557306"
FT CONFLICT 188..189
FT /note="AE -> R (in Ref. 2; CAA00968)"
FT /evidence="ECO:0000305"
FT HELIX 3..13
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 56..69
FT /evidence="ECO:0007829|PDB:1BS0"
FT TURN 77..80
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 84..97
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 108..119
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 134..141
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 143..150
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 155..163
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 170..177
FT /evidence="ECO:0007829|PDB:1BS0"
FT TURN 179..181
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 187..196
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 200..204
FT /evidence="ECO:0007829|PDB:1BS0"
FT TURN 206..211
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 219..222
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 228..236
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 243..247
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 249..258
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 260..263
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 270..284
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 286..306
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:1DJ9"
FT STRAND 318..320
FT /evidence="ECO:0007829|PDB:1BS0"
FT STRAND 323..327
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 328..340
FT /evidence="ECO:0007829|PDB:1BS0"
FT TURN 350..352
FT /evidence="ECO:0007829|PDB:1DJE"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:1BS0"
FT HELIX 370..383
FT /evidence="ECO:0007829|PDB:1BS0"
SQ SEQUENCE 384 AA; 41594 MW; D1AF5C054A5B4B06 CRC64;
MSWQEKINAA LDARRAADAL RRRYPVAQGA GRWLVADDRQ YLNFSSNDYL GLSHHPQIIR
AWQQGAEQFG IGSGGSGHVS GYSVVHQALE EELAEWLGYS RALLFISGFA ANQAVIAAMM
AKEDRIAADR LSHASLLEAA SLSPSQLRRF AHNDVTHLAR LLASPCPGQQ MVVTEGVFSM
DGDSAPLAEI QQVTQQHNGW LMVDDAHGTG VIGEQGRGSC WLQKVKPELL VVTFGKGFGV
SGAAVLCSST VADYLLQFAR HLIYSTSMPP AQAQALRASL AVIRSDEGDA RREKLAALIT
RFRAGVQDLP FTLADSCSAI QPLIVGDNSR ALQLAEKLRQ QGCWVTAIRP PTVPAGTARL
RLTLTAAHEM QDIDRLLEVL HGNG
