P12995 (BIOA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	bioA
Ordered Locus Names:	b0774, JW0757

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	429 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
Induction	Repressed by BirA. Ref.6 Ref.7 Ref.8 Ref.12
Miscellaneous	Catalysis proceeds by a classical ping-pong bi-bi reaction mechanism. HAMAP-Rule MF_00834
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 process	Biotin biosynthesis
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate S-adenosyl-L-methionine
Molecular function	Aminotransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	biotin biosynthetic process Inferred from direct assay Ref.5. Source: UniProtKB
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	adenosylmethionine-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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 429

429

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase HAMAP-Rule MF_00834

PRO_0000120366

Regions

Region

112 – 113

2

Pyridoxal phosphate binding HAMAP-Rule MF_00834

Region

308 – 309

2

Pyridoxal phosphate binding HAMAP-Rule MF_00834

Sites

Binding site

52

1

Substrate

Binding site

144

1

Substrate Probable

Binding site

245

1

Pyridoxal phosphate

Binding site

274

1

Substrate

Binding site

307

1

Substrate; via carbonyl oxygen

Binding site

391

1

Substrate

Site

17

1

Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM Probable

Amino acid modifications

Modified residue

274

1

N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_00834

Experimental info

Mutagenesis

17

1

Y → F: Severely reduces the aminotransferase activity. Ref.13

Mutagenesis

144

1

Y → F: Severely reduces the aminotransferase activity. Ref.13

Mutagenesis

147

1

D → N: Loss of aminotransferase activity. Ref.13

Mutagenesis

253

1

R → A: Has only a small effect on the rate of reaction with DAPA. Ref.13

Mutagenesis

253

1

R → K: Increases aminotransferase activity toward SAM. Ref.13

Mutagenesis

253

1

R → M: Loss of aminotransferase activity. Ref.13

Mutagenesis

253

1

R → Q: Increases aminotransferase activity toward SAM. Ref.13

Mutagenesis

391

1

R → A: Reduces aminotransferase activity. Ref.11

Sequence conflict

11

1

R → P in CAA00964. Ref.2

Sequence conflict

99 – 102

4

TPQP → SGRNA in AAA23514. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

429

Helix Strand Turn

Details...

Helix

3 – 12

10

Beta strand

20 – 22

3

Beta strand

27 – 34

8

Beta strand

36 – 39

4

Beta strand

44 – 49

6

Turn

50 – 54

5

Helix

62 – 74

13

Beta strand

81 – 84

4

Helix

86 – 98

13

Beta strand

105 – 111

7

Helix

112 – 130

19

Beta strand

136 – 140

5

Helix

149 – 152

4

Turn

157 – 161

5

Helix

162 – 165

4

Turn

166 – 168

3

Beta strand

173 – 175

3

Beta strand

180 – 184

5

Helix

188 – 191

4

Helix

192 – 201

10

Turn

202 – 204

3

Beta strand

205 – 210

6

Beta strand

212 – 215

4

Turn

217 – 219

3

Beta strand

221 – 223

3

Helix

226 – 238

13

Beta strand

241 – 245

5

Turn

247 – 254

8

Beta strand

255 – 258

4

Helix

259 – 263

5

Beta strand

268 – 272

5

Helix

274 – 277

4

Beta strand

279 – 281

3

Beta strand

284 – 288

5

Helix

290 – 297

8

Beta strand

299 – 303

5

Turn

309 – 312

4

Helix

314 – 328

15

Helix

332 – 347

16

Helix

348 – 352

5

Beta strand

356 – 362

7

Beta strand

365 – 372

8

Helix

376 – 385

10

Beta strand

396 – 399

4

Helix

407 – 420

14

Helix

424 – 426

3

Sequences

	Sequence		Length	Mass (Da)
	P12995 [UniParc]. Last modified October 1, 1994. Version 2. Checksum: 84D2D1AE3A1280FF	FASTA	429	47,336
	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

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]	"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.

PIR

XNECDP. F64813.

RefSeq

NP_415295.1. NC_000913.2.
YP_489047.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P12995.

SMR

P12995. Positions 1-429.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9219N.

IntAct

P12995. 5 interactions.

MINT

MINT-1275136.

STRING

511145.b0774.

Proteomic databases

PaxDb

P12995.

PRIDE

P12995.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73861; AAC73861; b0774.
BAE76361; BAE76361; BAE76361.

GeneID

12932847.
945376.

KEGG

ecj:Y75_p0747.
eco:b0774.

PATRIC

32116749. VBIEscCol129921_0800.

Organism-specific databases

EchoBASE

EB0115.

EcoGene

EG10117. bioA.

Phylogenomic databases

eggNOG

COG0161.

HOGENOM

HOG000020209.

KO

K00833.

OMA

DRVFYAD.

ProtClustDB

PRK07986.

Enzyme and pathway databases

BioCyc

EcoCyc:DAPASYN-MONOMER.
ECOL316407:JW0757-MONOMER.
MetaCyc:DAPASYN-MONOMER.

BRENDA

2.6.1.62. 2026.

SABIO-RK

P12995.

UniPathway

UPA00078; UER00160.

Gene expression databases

Genevestigator

P12995.

Family and domain databases

Gene3D

3.40.640.10. 1 hit.
3.90.1150.10. 2 hits.

HAMAP

MF_00834. BioA.

InterPro

IPR005814. Aminotrans_3.
IPR005815. BioA.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]

PANTHER

PTHR11986. PTHR11986. 1 hit.
PTHR11986:SF8. PTHR11986:SF8. 1 hit.

Pfam

PF00202. Aminotran_3. 1 hit.
[Graphical view]

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

TIGRFAMs

TIGR00508. bioA. 1 hit.

PROSITE

PS00600. AA_TRANSFER_CLASS_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P12995.

Entry information

Entry name

BIOA_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 131 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program