8-amino-7-oxononanoate synthase
8-Amino-7-oxononanoate synthase (AONS) is a pyridoxal 5′-phosphate-dependent enzyme that catalyzes the decarboxylative condensation of L-alanine with pimeloyl-CoA in a stereospecific manner to form 8(S)-amino-7-oxononanoate, coenzyme A, and carbon dioxide in the first committed step of biotin biosynthesis. AONS also performs the carboxylation of acetyl-CoA to give malonyl-CoA, which is the first step in fatty acid biosynthesis.
Biotin is an essential enzyme cofactor for carboxylase and transcarboxlase reactions. Fatty acid synthesis is essential for the growth and development of most organisms. Plants, microorganisms, and some fungi bio-synthesize their own biotin, whilst animals require trace amounts in their diet, thus, inhibition of the enzymes involved in the biotin biosynthesis pathway can cause irreparable damage to plants but can be non-toxic to mammals; for this reason, such enzymes can be useful targets for the rational design of inhibitors in the hopes of finding new herbicides and antibiotics.
Reference Protein and Structure
- Sequence
-
P12998
(2.3.1.47)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Escherichia coli K-12 (Bacteria)
- PDB
-
1bs0
- PLP-DEPENDENT ACYL-COA SYNTHASE
(1.65 Å)
- Catalytic CATH Domains
-
3.40.640.10
3.90.1150.10
(see all for 1bs0)
- Cofactors
- Pyridoxal 5'-phosphate(2-) (1)
Enzyme Reaction (EC:2.3.1.47)
+
+
→
+
+
Alternative enzyme names: 7-keto-8-aminopelargonic acid synthetase, 7-keto-8-aminopelargonic synthetase, 8-amino-7-oxopelargonate synthase, 8-amino-7-ketopelargonate synthase, AONS, 7-KAP synthetase, BioF (gene name),
Enzyme Mechanism
Introduction
The mechanism of AONS catalysis appears to be similar to those of other PLP-dependent enzymes. The catalysed reaction involves an acylation step with inversion of configuration and a decarboxylation with retention of configuration. The steps involved are as follows:
- Formation of the Ala-PLP aldimine. The first step corresponds to the formation of the external aldimine with L-alanine.
- Formation of the Ala quinonoid. After binding of pimeloyl-CoA, which induces a conformational change, the Ala quinonoid is formed by abstraction of the C2-proton on the Si-face of the PLP aldimine by the active site lysine (the Si-face refers to the C4' (carbonyl) prochiral trigonal carbon of the PLP).
- Formation of the intermediate. The acylation is thought to take place with inversion of configuration, although this has never been directly proved.
- Decarboxylation and reprotonation. The intermediate is then decarboxylated to yield the second quinonoid species. It is not yet known what is the position of the carbon-carbon bond before decarboxylation: either parallel to the PLP pi-system or to the AON carbonyl pi-orbitals, for facile rupture of the C-C bond (stereoelectronic principle). Reprotonation on the Si-face, likely catalysed by the active site lysine, yields the AON external aldimine.
- Product release. The AON product is then released by transaldimination by the active site lysine. The configuration of the AON product was proposed to be (S), based on the configuration of (+)-biotin. However, this compound racemizes quickly even at neutral pH.
Catalytic Residues Roles
| UniProt | PDB* (1bs0) | ||
| Lys236 | Lys236A | Covalently bound to the PLP cofactor; acts as a general acid/base. | covalent catalysis, proton shuttle (general acid/base) |
| Ser179 | Ser179A | Activates the general acid/base histidine (His207) to act in the decarboxylation step. | modifies pKa |
| Asp204 | Asp204A | Acts to stabilise the N of the pyrimidine ring during catalysis. | electrostatic stabiliser |
| His207 | His207A | Thought to act as a general acid/base in the decarboxylation step. | proton shuttle (general acid/base), electrostatic stabiliser |
| His133 | His133A | His133 is in a parallel, stacked arrangement with the PLP ring. This interaction with the PLP plane and holds it in position, which exposes the reactive O3′ and C4′ of the pyridine ring towards the lysine residue and the substrates. Also thought to act as a general acid/base during the reaction. | proton shuttle (general acid/base), electrostatic stabiliser |
| Glu175 | Glu175A | Polarises the serine (Ser179), which helps activate the general acid/base histidine (His207) for the decarboxylation step. | electrostatic stabiliser |
| Asn47 | Asn47A | Acts to stabilise the negatively charged intermediate that subsequently undergoes decarboxylation. | electrostatic stabiliser |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Mann S et al. (2011), Biochim Biophys Acta, 1814, 1459-1466. Pyridoxal-5′-phosphate-dependent enzymes involved in biotin biosynthesis: Structure, reaction mechanism and inhibition. DOI:10.1016/j.bbapap.2010.12.004. PMID:21182990.
- Hahn HG et al. (2015), Pestic Biochem Physiol, 125, 78-83. Triazolyl phenyl disulfides: 8-Amino-7-oxononanoate synthase inhibitors as potential herbicides. DOI:10.1016/j.pestbp.2015.05.006. PMID:26615154.
- Lin S et al. (2010), Nat Chem Biol, 6, 682-688. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. DOI:10.1038/nchembio.420. PMID:20693992.
- Kerbarh O et al. (2006), Chem Commun (Camb), 60-62. Mechanism of α-oxoamine synthases: identification of the intermediate Claisen product in the 8-amino-7-oxononanoate synthase reaction. DOI:10.1039/b511837a. PMID:16353092.
- Alexeev D et al. (2006), Org Biomol Chem, 4, 1209-. Suicide inhibition of α-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine. DOI:10.1039/b517922j. PMID:16557306.
- Webster SP et al. (2000), Biochemistry, 39, 516-528. Mechanism of 8-Amino-7-oxononanoate Synthase: Spectroscopic, Kinetic, and Crystallographic Studies†,‡. DOI:10.1021/bi991620j.
- Alexeev D et al. (1998), J Mol Biol, 284, 401-419. The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme. DOI:10.1006/jmbi.1998.2086. PMID:9813126.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| His133A | electrostatic stabiliser, proton shuttle (general acid/base) |
| Lys236A | covalent catalysis, proton shuttle (general acid/base) |
| Asn47A | electrostatic stabiliser |
| Glu175A | electrostatic stabiliser |
| Ser179A | modifies pKa |
| Asp204A | electrostatic stabiliser |
| His207A | proton shuttle (general acid/base), electrostatic stabiliser |