EzCatDB: D00092

DB codeD00092
RLCP classification6.30.115000.5080
3.1187.70500.5510
6.40.500000.5200
CATH domainDomain 13.90.1150.10Catalytic domain
Domain 23.40.640.10Catalytic domain
E.C.2.3.1.47
CSA1bs0

CATH domainRelated DB codes (homologues)
3.40.640.10D00085,D00101,D00102,D00103,D00104,D00107,D00108,D00109,D00255,D00257,D00258,D00265,D00269,D00515,M00031,D00279
3.90.1150.10D00085,D00101,D00102,D00103,D00104,D00107,D00108,D00109,D00255,D00257,D00258,D00265,D00269,D00515,M00031,D00279

Enzyme Name
Swiss-protKEGG

P12998
Protein name8-amino-7-oxononanoate synthase8-amino-7-oxononanoate synthase
7-keto-8-aminopelargonic acid synthetase
7-keto-8-aminopelargonic synthetase
8-amino-7-oxopelargonate synthase
SynonymsAONS
EC 2.3.1.47
8-amino-7-ketopelargonate synthase
7-keto-8-amino-pelargonic acid synthetase
7-KAP synthetase
L-alanine--pimelyl-CoA ligase

KEGG pathways
MAP codePathways
MAP00780Biotin metabolism

Swiss-prot:Accession NumberP12998
Entry nameBIOF_ECOLI
Activity6-carboxyhexanoyl-CoA + L-alanine = 8-amino-7- oxononanoate + CoA + CO(2).
SubunitHomodimer.
Subcellular location
CofactorPyridoxal phosphate.


CofactorsSubstratesProductsintermediates
KEGG-idC00018C01063C00041C01092C00010C00011I00049I00032I00050I00051I00052
CompoundPyridoxal phosphate6-Carboxyhexanoyl-CoAL-Alanine8-Amino-7-oxononanoateCoACO2External 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)
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamine group,carbohydrate,fatty acid,nucleotide,peptide/protein,sulfide groupamino acidsamino acids,carbohydrate,fatty acidamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl groupothers




1bs0A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dj9A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1djeA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2g6wA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1bs0A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dj9A02Analogue:KAMUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:KAM
1djeA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2g6wA02Analogue:LLFUnboundUnbound
UnboundUnboundIntermediate-analogue:LLFUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [4]
pdbCatalytic residuesCofactor-binding residues
1bs0A01ASN 47

1dj9A01ASN 47

1djeA01ASN 47

2g6wA01ASN 47

1bs0A02HIS 133;GLU 175;SER 179;HIS 207;LYS 236
LYS 236(PLP binding)
1dj9A02HIS 133;GLU 175;SER 179;HIS 207;LYS 236
LYS 236(PLP binding)
1djeA02HIS 133;GLU 175;SER 179;HIS 207;LYS 236
LYS 236(PLP binding)
2g6wA02HIS 133;GLU 175;SER 179;HIS 207;LYS 236
LYS 236(PLP binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.412
[4]Fig.37
[5]Fig.89

references
[1]
PubMed ID9451826
JournalInt J Biochem Cell Biol
Year1997
Volume29
Pages1285-95
AuthorsBorkow G, Arion D, Noronha A, Scartozzi M, Damha MJ, Parniak MA
TitleInhibitory potency of R-region specific antisense oligonucleotides against in vitro DNA polymerization and template-switching reactions catalysed by HIV-1 reverse transcriptase.
[2]
PubMed ID9765987
JournalBiochem Soc Trans
Year1998
Volume26
PagesS268
AuthorsWebster SP, Campopiano DJ, Alexeev D, Alexeeva M, Watt RM, Sawyer L, Baxter RL
TitleCharacterisation of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl CoA condensing enzyme.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS)
Medline ID99033055
PubMed ID9813126
JournalJ Mol Biol
Year1998
Volume284
Pages401-19
AuthorsAlexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L
TitleThe crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme.
Related PDB1bs0
Related Swiss-protP12998
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS)
PubMed ID10642176
JournalBiochemistry
Year2000
Volume39
Pages516-28
AuthorsWebster SP, Alexeev D, Campopiano DJ, Watt RM, Alexeeva M, Sawyer L, Baxter RL
TitleMechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies.
Related PDB1dj9,1dje
[5]
PubMed ID11318637
JournalBiochemistry
Year2001
Volume40
Pages5151-60
AuthorsSchmidt A, Sivaraman J, Li Y, Larocque R, Barbosa JA, Smith C, Matte A, Schrag JD, Cygler M
TitleThree-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
[6]
PubMed ID16557306
JournalOrg Biomol Chem
Year2006
Volume4
Pages1209-12
AuthorsAlexeev D, Baxter RL, Campopiano DJ, Kerbarh O, Sawyer L, Tomczyk N, Watt R, Webster SP
TitleSuicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine.
Related PDB2g6w

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.

createdupdated
2004-03-172009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.