DB code: D00092

RLCP classification	6.30.115000.5080 : Double-bonded atom exchange
	3.1187.70500.5510 : Transfer
	6.40.500000.5200 : Double-bonded atom exchange
CATH domain	3.90.1150.10 : Aspartate Aminotransferase, domain 1	Catalytic domain
CATH domain	3.40.640.10 : Aspartate Aminotransferase; domain 2	Catalytic domain
E.C.	2.3.1.47
CSA	1bs0
M-CSA	1bs0
MACiE

CATH domain	Related DB codes (homologues)
3.40.640.10 : Aspartate Aminotransferase; domain 2	D00085 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00255 D00257 D00258 D00265 D00269 D00515 M00031 D00279
3.90.1150.10 : Aspartate Aminotransferase, domain 1	D00085 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00255 D00257 D00258 D00265 D00269 D00515 M00031 D00279

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P12998	8-amino-7-oxononanoate synthase	AONS EC 2.3.1.47 7-keto-8-amino-pelargonic acid synthase 7-KAP synthase KAPA synthase 8-amino-7-ketopelargonate synthase	NP_415297.1 (Protein) NC_000913.2 (DNA/RNA sequence) YP_489049.1 (Protein) NC_007779.1 (DNA/RNA sequence)	PF00155 (Aminotran_1_2) [Graphical View]

KEGG enzyme name
8-amino-7-oxononanoate synthase 7-keto-8-aminopelargonic acid synthetase 7-keto-8-aminopelargonic synthetase 8-amino-7-oxopelargonate synthase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P12998	BIOF_ECOLI	6-carboxyhexanoyl-CoA + L-alanine = 8-amino-7- oxononanoate + CoA + CO(2).	Homodimer.		Pyridoxal phosphate.

KEGG Pathways
Map code	Pathways	E.C.
MAP00780	Biotin metabolism

Compound table
	Cofactors	Substrates		Products			Intermediates
KEGG-id	C00018	C01063	C00041	C01092	C00010	C00011	I00049	I00032	I00050	I00051	I00052
E.C.
Compound	Pyridoxal phosphate	6-Carboxyhexanoyl-CoA	L-Alanine	8-Amino-7-oxononanoate	CoA	CO2	External aldimine intermediate (PLP-L-Ala)	Quinonoid Intermediate (PLP-Ala)	External aldimine intermediate (PLP-beta-ketoacid-oxononanoate)	Quinonoid intermediate (PLP-Amino-oxononanoate)	External aldimine intermediate (final stage:PLP-Amino-oxononanoate)
Type	aromatic ring (with nitrogen atoms),phosphate group/phosphate ion	amine group,carbohydrate,fatty acid,nucleotide ,peptide/protein,sulfide group	amino acids	amino acids,carbohydrate,fatty acid	amine group,carbohydrate,nucleotide ,peptide/protein,sulfhydryl group	others
ChEBI	18405 18405	15504 15504	16977 57972 16977 57972	15830 57532 15830 57532	15346 15346	16526 16526
PubChem	1051 1051	3082140 439385 3082140 439385	5950 7311724 5950 7311724	173 25244029 173 25244029	6816 87642 6816 87642	280 280

1bs0A01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1dj9A01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1djeA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2g6wA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1bs0A02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1dj9A02	Analogue:KAM	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:KAM
1djeA02	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2g6wA02	Analogue:LLF	Unbound	Unbound		Unbound	Unbound	Intermediate-analogue:LLF	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [4]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1bs0A01	ASN 47
1dj9A01	ASN 47
1djeA01	ASN 47
2g6wA01	ASN 47
1bs0A02	HIS 133;GLU 175;SER 179;HIS 207;LYS 236	LYS 236(PLP binding)
1dj9A02	HIS 133;GLU 175;SER 179;HIS 207;LYS 236	LYS 236(PLP binding)
1djeA02	HIS 133;GLU 175;SER 179;HIS 207;LYS 236	LYS 236(PLP binding)
2g6wA02	HIS 133;GLU 175;SER 179;HIS 207;LYS 236	LYS 236(PLP binding)

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[3]	p.412
[4]	Fig.3	7
[5]	Fig.8	9

References
[1]
Resource
Comments
Medline ID
PubMed ID	9451826
Journal	Int J Biochem Cell Biol
Year	1997
Volume	29
Pages	1285-95
Authors	Borkow G, Arion D, Noronha A, Scartozzi M, Damha MJ, Parniak MA
Title	Inhibitory potency of R-region specific antisense oligonucleotides against in vitro DNA polymerization and template-switching reactions catalysed by HIV-1 reverse transcriptase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	9765987
Journal	Biochem Soc Trans
Year	1998
Volume	26
Pages	S268
Authors	Webster SP, Campopiano DJ, Alexeev D, Alexeeva M, Watt RM, Sawyer L, Baxter RL
Title	Characterisation of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl CoA condensing enzyme.
Related PDB
Related UniProtKB
[3]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS)
Medline ID	99033055
PubMed ID	9813126
Journal	J Mol Biol
Year	1998
Volume	284
Pages	401-19
Authors	Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L
Title	The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme.
Related PDB	1bs0
Related UniProtKB	P12998
[4]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS)
Medline ID
PubMed ID	10642176
Journal	Biochemistry
Year	2000
Volume	39
Pages	516-28
Authors	Webster SP, Alexeev D, Campopiano DJ, Watt RM, Alexeeva M, Sawyer L, Baxter RL
Title	Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies.
Related PDB	1dj9 1dje
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	11318637
Journal	Biochemistry
Year	2001
Volume	40
Pages	5151-60
Authors	Schmidt A, Sivaraman J, Li Y, Larocque R, Barbosa JA, Smith C, Matte A, Schrag JD, Cygler M
Title	Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	16557306
Journal	Org Biomol Chem
Year	2006
Volume	4
Pages	1209-12
Authors	Alexeev D, Baxter RL, Campopiano DJ, Kerbarh O, Sawyer L, Tomczyk N, Watt R, Webster SP
Title	Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine.
Related PDB	2g6w
Related UniProtKB

Comments
This enzyme belongs to the class-II aminotransferase family. According to the literature [4], this enzyme catalyzes the following reactions: (A) Formation of external aldimine (with substrate alanine), (B) Transfer of acyl group to the alpha-carbon of the alanine-PLP complex, (C) Elimination of carboxylate group, (D) Isomerization (shift of double-bond position): (E) Reformation of internal aldimine with Lys236. These reactions proceed in the following way. (A) Formation of external aldimine occurs as follows: (A1) The hydrogen-bonding network, composed of His207/Ser179/Glu175, keeps the O3 atom of PLP negatively charged. (A2) The negatively charged O3 atom of PLP acts as a general base, to deprotonate the amino group of substrate, L-alanine. The abstracted proton is donated to NZ nitrogen of Lys236. (A3) The deprotonated amine group of L-alanine makes a nucleophilic attack on the C4A carbon of PLP, forming a transient diamine intermediate. (A4) There must be a general base, which deprotonates the amine group of the previously alanine substrate, so that the lone pair of the amine group can attack on the C4A atom to form a double-bond, and to release the amine of the catalytic residue, Lys236. Considering the active-site structure, His133 may play the role as the general base, although the literature has not mentioned it. (The released Lys236 must be deprotonated, so that it can act as a general base at the next stage.) (B) Transfer of acyl group proceeds as follows: (B1) Lys236 acts as a general base, which abstracts a proton from alpha-carbon of alanine (covalently bound to PLP), leading to the formation of a quinonoid intermediate. Here, the intermediate is stabilized by its resonance. (B2) The transferred group, acyl group of the second substrate, Pimeloyl-CoA, is stabilized by His133. (B3) The activated acceptor group, the alpha-carbon (sp2; double-bonde), makes a nucleophilic attack on the acyl carbon atom, releasing a product, CoAS(H). (C) According to the literature [4], the mechanism of elimination of carboxylate group (decarboxylation) for this enzyme is unknown. However, the literature [4] mentioned that the reaction involves an electron sink, which is formed by the protonation to C7 ketone by His133. Moreover, Asn47 might stabilize the negative charge of the carboxylate. (D) Isomerization (shift of double-bond position): (D1) Lys236 acts as a general acid to protonate the alpha-carbon, leading to the external aldimine. (E) Reformation of internal aldimine with Lys236 is the reverse reaction of the formation of external aldimine (A): (E1) The deprotonated Lys236 acts as a nucleophile, which attacks on the C4A atom of PLP, forming a diamine intermediate. (E2) There must be a general acid, to protonate the amine from the product. (His133 might play the role.) (E3) The negatively charged O3 atom of PLP abstracts a proton from the nitrogen of Lys236, and then protonates the nitrogen atom from the product, so that the lone pair of Lys236 attacks on the C4A atom to form a double-bond again, and to release the product amine group. (E4) The hydrogen-bonding network, composed of His207/Ser179/Glu175, must keep the O3 atom of PLP negatively charged during this reaction.

Comments

This enzyme belongs to the class-II aminotransferase family.
According to the literature [4], this enzyme catalyzes the following reactions:
(A) Formation of external aldimine (with substrate alanine),
(B) Transfer of acyl group to the alpha-carbon of the alanine-PLP complex,
(C) Elimination of carboxylate group,
(D) Isomerization (shift of double-bond position):
(E) Reformation of internal aldimine with Lys236.
These reactions proceed in the following way.
(A) Formation of external aldimine occurs as follows:
(A1) The hydrogen-bonding network, composed of His207/Ser179/Glu175, keeps the O3 atom of PLP negatively charged.
(A2) The negatively charged O3 atom of PLP acts as a general base, to deprotonate the amino group of substrate, L-alanine. The abstracted proton is donated to NZ nitrogen of Lys236.
(A3) The deprotonated amine group of L-alanine makes a nucleophilic attack on the C4A carbon of PLP, forming a transient diamine intermediate.
(A4) There must be a general base, which deprotonates the amine group of the previously alanine substrate, so that the lone pair of the amine group can attack on the C4A atom to form a double-bond, and to release the amine of the catalytic residue, Lys236. Considering the active-site structure, His133 may play the role as the general base, although the literature has not mentioned it. (The released Lys236 must be deprotonated, so that it can act as a general base at the next stage.)
(B) Transfer of acyl group proceeds as follows:
(B1) Lys236 acts as a general base, which abstracts a proton from alpha-carbon of alanine (covalently bound to PLP), leading to the formation of a quinonoid intermediate. Here, the intermediate is stabilized by its resonance.
(B2) The transferred group, acyl group of the second substrate, Pimeloyl-CoA, is stabilized by His133.
(B3) The activated acceptor group, the alpha-carbon (sp2; double-bonde), makes a nucleophilic attack on the acyl carbon atom, releasing a product, CoAS(H).
(C) According to the literature [4], the mechanism of elimination of carboxylate group (decarboxylation) for this enzyme is unknown. However, the literature [4] mentioned that the reaction involves an electron sink, which is formed by the protonation to C7 ketone by His133. Moreover, Asn47 might stabilize the negative charge of the carboxylate.
(D) Isomerization (shift of double-bond position):
(D1) Lys236 acts as a general acid to protonate the alpha-carbon, leading to the external aldimine.
(E) Reformation of internal aldimine with Lys236 is the reverse reaction of the formation of external aldimine (A):
(E1) The deprotonated Lys236 acts as a nucleophile, which attacks on the C4A atom of PLP, forming a diamine intermediate.
(E2) There must be a general acid, to protonate the amine from the product. (His133 might play the role.)
(E3) The negatively charged O3 atom of PLP abstracts a proton from the nitrogen of Lys236, and then protonates the nitrogen atom from the product, so that the lone pair of Lys236 attacks on the C4A atom to form a double-bond again, and to release the product amine group.
(E4) The hydrogen-bonding network, composed of His207/Ser179/Glu175, must keep the O3 atom of PLP negatively charged during this reaction.

Created	Updated
2004-03-17	2009-02-26