8-amino-7-oxononanoate synthase - Escherichia coli (strain K12)

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P12998 (BIOF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 122. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
8-amino-7-oxononanoate synthase
Short name=AONS
EC=2.3.1.47

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 names

Name:	bioF
Ordered Locus Names:	b0776, JW0759

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	384 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7
Catalytic activity	Pimeloyl-[acyl-carrier protein] + L-alanine = 8-amino-7-oxononanoate + CO₂ + holo-[acyl-carrier protein]. Ref.7
Cofactor	Pyridoxal phosphate. Ref.5
Enzyme regulation	Competitively inhibited by D-alanine, 8-amino-7-hydroxy-8-phosphonononanoic acid and 2-amino-3-hydroxy-2-methylnonadioic acid. Ref.6
Pathway	Cofactor biosynthesis; biotin biosynthesis. HAMAP-Rule MF_01693
Subunit structure	Homodimer. Ref.8
Sequence similarities	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=25 µM for pimeloyl-CoA (at pH 7.5 and at 30 degrees Celsius) Ref.5 K_M=0.5 µM for L-alanine (at pH 7.5 and at 30 degrees Celsius)
Mass spectrometry	Molecular mass is 41464.4±4.5 Da from positions 2 - 384. Determined by ESI. Ref.5

Ontologies

Keywords
Biological process	Biotin biosynthesis
Ligand	Pyridoxal phosphate
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	biotin biosynthetic process Inferred from mutant phenotype PubMed 4921685. Source: EcoCyc
Molecular_function	8-amino-7-oxononanoate synthase activity Inferred from direct assay Ref.5. Source: EcoCyc pyridoxal phosphate binding Inferred from direct assay Ref.5. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5

Chain

2 – 384

383

8-amino-7-oxononanoate synthase HAMAP-Rule MF_01693

PRO_0000163811

Regions

Region

108 – 109

Pyridoxal phosphate binding HAMAP-Rule MF_01693

Region

204 – 207

Pyridoxal phosphate binding HAMAP-Rule MF_01693

Region

233 – 236

Pyridoxal phosphate binding HAMAP-Rule MF_01693

Sites

Binding site

Substrate

Binding site

133

Substrate

Binding site

179

Pyridoxal phosphate

Binding site

352

Substrate

Amino acid modifications

Modified residue

236

N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_01693

Experimental info

Sequence conflict

188 – 189

AE → R in CAA00968. Ref.2

Secondary structure

384

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P12998 [UniParc].

Last modified January 1, 1990. Version 1.
Checksum: D1AF5C054A5B4B06
Show »

FASTA

384

41,594

        10         20         30         40         50         60 
MSWQEKINAA LDARRAADAL RRRYPVAQGA GRWLVADDRQ YLNFSSNDYL GLSHHPQIIR 

        70         80         90        100        110        120 
AWQQGAEQFG IGSGGSGHVS GYSVVHQALE EELAEWLGYS RALLFISGFA ANQAVIAAMM 

       130        140        150        160        170        180 
AKEDRIAADR LSHASLLEAA SLSPSQLRRF AHNDVTHLAR LLASPCPGQQ MVVTEGVFSM 

       190        200        210        220        230        240 
DGDSAPLAEI QQVTQQHNGW LMVDDAHGTG VIGEQGRGSC WLQKVKPELL VVTFGKGFGV 

       250        260        270        280        290        300 
SGAAVLCSST VADYLLQFAR HLIYSTSMPP AQAQALRASL AVIRSDEGDA RREKLAALIT 

       310        320        330        340        350        360 
RFRAGVQDLP FTLADSCSAI QPLIVGDNSR ALQLAEKLRQ QGCWVTAIRP PTVPAGTARL 

       370        380 
RLTLTAAHEM QDIDRLLEVL HGNG

« Hide

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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]	"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J04423 Genomic DNA. Translation: AAA23516.1.
A11542 Unassigned DNA. Translation: CAA00968.1.
U00096 Genomic DNA. Translation: AAC73863.1.
AP009048 Genomic DNA. Translation: BAE76363.1.

PIR

SYECKP. D32025.

RefSeq

NP_415297.1. NC_000913.2.
YP_489049.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P12998.

SMR

P12998. Positions 2-384.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6870N.

IntAct

P12998. 2 interactions.

STRING

511145.b0776.

Proteomic databases

PaxDb

P12998.

PRIDE

P12998.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73863; AAC73863; b0776.
BAE76363; BAE76363; BAE76363.

GeneID

12930959.
945384.

KEGG

ecj:Y75_p0749.
eco:b0776.

PATRIC

32116753. VBIEscCol129921_0802.

Organism-specific databases

EchoBASE

EB0119.

EcoGene

EG10121. bioF.

Phylogenomic databases

eggNOG

COG0156.

HOGENOM

HOG000221021.

K00652.

OMA

DFYAITQ.

ProtClustDB

PRK05958.

Enzyme and pathway databases

BioCyc

EcoCyc:7KAPSYN-MONOMER.
ECOL316407:JW0759-MONOMER.
MetaCyc:7KAPSYN-MONOMER.

UniPathway

UPA00078.

Gene expression databases

Genevestigator

P12998.

Family and domain databases

Gene3D

3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.

HAMAP

MF_01693. BioF_aminotrans_2.

InterPro

IPR022834. Amino_oxononanoate_synth.
IPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR004723. BioF.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]

Pfam

PF00155. Aminotran_1_2. 1 hit.
[Graphical view]

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

TIGRFAMs

TIGR00858. bioF. 1 hit.

PROSITE

PS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P12998.

Entry information

Entry name

BIOF_ECOLI

Accession

Primary (citable) accession number: P12998
Secondary accession number(s): Q2MBJ3

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	May 1, 2013
This is version 122 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents