DB code: D00092

RLCP classification 6.40.500000.5600 : Double-bonded atom exchange
3.1187.70500.5510 : Transfer
6.30.115000.5080 : Double-bonded atom exchange
CATH domain 3.90.1150.10 : Aspartate Aminotransferase, domain 1 Catalytic 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)
3.90.1150.10 : Aspartate Aminotransferase, domain 1 D00085 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00255 D00257 D00258 D00265 D00269 D00515 M00031 D00279
3.40.640.10 : Aspartate Aminotransferase; domain 2 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
15504
16977
57972
15830
57532
15346
16526
PubChem 1051
3082140
439385
5950
7311724
173
25244029
6816
87642
280
1bs0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dj9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1djeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2g6wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bs0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dj9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:KAM Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:KAM
1djeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2g6wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 47
1dj9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 47
1djeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 47
2g6wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 47
1bs0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 133;GLU 175;SER 179;HIS 207;LYS 236 LYS 236(PLP binding)
1dj9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 133;GLU 175;SER 179;HIS 207;LYS 236 LYS 236(PLP binding)
1djeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 133;GLU 175;SER 179;HIS 207;LYS 236 LYS 236(PLP binding)
2g6wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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.

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