Adenosylmethionine--8-amino-7-oxononanoate transaminase

 

Adenosylmethionine--8-amino-7-oxononanoate transaminase (BioA) is a PLP-dependent enzyme that functions in biotin synthesis. It utilises S-adenosyl-L-methionine (SAM) to transaminate the biotin precurson 7-keto-8-aminopelargonic acid and form the next intermediate in the pathway, 7, 8-diaminopelargonic acid. It is the only animotransferase known to utilise SAM as an amino donor. S-adenosylhomocysteine can also act as donor. SAM is a costly metabolite, however, due to the fact that the aminotransferase-catalyzed reactions are most efficient when the pKa of the substrate and the enzyme are separated, SAM may be the only substrate available with an appropriate pKa [PMID:12379100].

 

Reference Protein and Structure

Sequence
P12995 UniProt (2.6.1.62) IPR005815 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1dty - CRYSTAL STRUCTURE OF ADENOSYLMETHIONINE-8-AMINO-7-OXONANOATE AMINOTRANSFERASE WITH PYRIDOXAL PHOSPHATE COFACTOR. (2.14 Å) PDBe PDBsum 1dty
Catalytic CATH Domains
3.40.640.10 CATHdb 3.90.1150.10 CATHdb (see all for 1dty)
Cofactors
Pyridoxal 5'-phosphate(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:2.6.1.62)

8-amino-7-oxononanoic acid zwitterion
CHEBI:57532ChEBI
+
S-adenosyl-L-methionine zwitterion
CHEBI:59789ChEBI
→
S-adenosyl-4-methylthio-2-oxobutanoate
CHEBI:16490ChEBI
+
7,8-diaminononanoate cation
CHEBI:58500ChEBI
Alternative enzyme names: 7,8-diaminonanoate transaminase, 7,8-diaminononanoate transaminase, 7,8-diaminopelargonic acid aminotransferase, 7-keto-8-aminopelargonic acid, 7-keto-8-aminopelargonic acid aminotransferase, DAPA aminotransferase, DAPA transaminase, Diaminopelargonate synthase, Adenosylmethionine--8-amino-7-oxononanoate aminotransferase, 7,8-diaminononanoate aminotransferase, 7,8-diamino-pelargonic acid aminotransferase,

Enzyme Mechanism

Introduction

Catalysis proceeds by a classical ping-pong bi-bi reaction mechanism. In the first steps, as in other PLP-dependent enzymes, the substrate SAM replaces Lys274 on the PLP-cofactor. Lys274 then deprotonates the CH adjacent to the bound amine, resulting in double bond rearrangement as the PLP acts as an electron sink. The PLP feeds the electrons back, resulting in the C=C attached to the aromatic ring deprotonates Lys274. Lys274 deprotonates water, which initiates a nucleophilic attack on the carbon of the C=N group in an addition reaction. The secondary amine deprotonates the attached hydroxyl group, initiating an elimination which releases S-adenosyl-4-methylthio-2-oxobutanoate. In the second phase, a Schiff base is formed between the free cofactor and 8-amino-7-oxononanoate. Lys274 then deprotonates the CH2 adjacent to the nitrogen, resulting in double bond rearrangement as the PLP acts as an electron sink. The PLP feeds the electrons back, the N+=C bond deprotonates Lys274. In the final steps of the reaction, Lys274 initiates a transaldimination resulting in the regenerated PLP cofactor and release of the 7,8-diaminononanoate poduct.

Catalytic Residues Roles

UniProt PDB* (1dty)
Tyr17 Tyr17A Only active in the second phase of the reaction. It acts to hold the second substrate in the correct orientation for the reaction to occur as well as stabilising the reactive intermediates formed during the course of the second phase of the mechanism. hydrogen bond acceptor, hydrogen bond donor, electrostatic stabiliser, steric role
Tyr144 Tyr144A Acts to hold the free cofactor in the correct orientation to ensure that the correct reactions occur. van der waals interaction, hydrogen bond acceptor, steric role
Asp245 Asp245A Helps stabilise the PLP cofactor to activate it as an electron sink. increase basicity, hydrogen bond acceptor, electrostatic stabiliser, steric role
Lys274 Lys274A The main catalytic residue, in the ground state of the enzyme it is covalently attached to the PLP coafactor. During the course of the reaction it is eliminated from the cofactor, allowing it to act as a general acid/base. It acts as a nucleophile in the final transaldimination reaction. covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, proton acceptor, proton donor, nucleophile, electron pair acceptor, electron pair donor
*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

bimolecular nucleophilic addition, proton transfer, overall reactant used, cofactor used, enzyme-substrate complex formation, intermediate formation, unimolecular elimination by the conjugate base, enzyme-substrate complex cleavage, intermediate collapse, intramolecular elimination, overall product formed, dehydration, schiff base formed, intermediate terminated, native state of cofactor regenerated, native state of enzyme regenerated

References

  1. Eliot AC et al. (2002), Biochemistry, 41, 12582-12589. The Dual-Specific Active Site of 7,8-Diaminopelargonic Acid Synthase and the Effect of the R391A Mutation†. DOI:10.1021/bi026339a. PMID:12379100.
  2. 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.
  3. Sandmark J et al. (2004), Biochemistry, 43, 1213-1222. Conserved and Nonconserved Residues in the Substrate Binding Site of 7,8-Diaminopelargonic Acid Synthase fromEscherichia coliAre Essential for Catalysis†. DOI:10.1021/bi0358059. PMID:14756557.
  4. Käck H et al. (1999), J Mol Biol, 291, 857-876. Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5′-phosphate-dependent enzymes. DOI:10.1006/jmbi.1999.2997. PMID:10452893.

Step 1. The amine of the substrate SAM attacks the PLP cofactor in a nucleophilic addition and the bound Lys274 deprotonates the newly attached amine.

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Catalytic Residues Roles

Residue Roles
Lys274A covalently attached, hydrogen bond acceptor, hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction
Lys274A proton acceptor, electron pair acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, overall reactant used, cofactor used, enzyme-substrate complex formation, intermediate formation

Step 2. The secondary amine that results from the initial attack initiates an elimination of the covalently bound lysine, resulting in free PLP and lysine in a neutral state.

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Catalytic Residues Roles

Residue Roles
Lys274A hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction
Lys274A nucleofuge

Chemical Components

ingold: unimolecular elimination by the conjugate base, enzyme-substrate complex cleavage, intermediate collapse, intermediate formation

Step 3. Lys274 deprotonates the CH adjacent to the bound amine, resulting in double bond rearrangement as the PLP acts as an electron sink.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys274A hydrogen bond acceptor, hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction
Lys274A proton acceptor

Chemical Components

proton transfer, intermediate formation

Step 4. The PLP feeds the electrons back, resulting in the C=C attached to the aromatic ring deprotonates Lys274.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys274A hydrogen bond donor
Asp245A hydrogen bond acceptor, increase basicity
Tyr144A steric role, van der waals interaction
Lys274A proton donor

Chemical Components

proton transfer, intermediate formation

Step 5. Lys274 deprotonates water, which initiates a nucleophilic attack on the carbon of the C=N group in an addition reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys274A hydrogen bond acceptor, hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction
Lys274A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation

Step 6. The secondary amine deprotonates the attached hydroxyl group, initiating an elimination which releases S-adenosyl-4-methylthio-2-oxobutanoate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys274A hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction

Chemical Components

ingold: intramolecular elimination, overall product formed, intermediate collapse, intermediate formation

Step 7. The amine of PMP initiates a nucleophilic attack on the carbonyl carbon of 8-amino-7-oxononanoate. The oxyanion deprotonates the newly formed secondary amine in the first step of a Schiff base formation.

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Catalytic Residues Roles

Residue Roles
Tyr17A hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Lys274A hydrogen bond donor
Asp245A steric role, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction, hydrogen bond acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 8. The secondary amine initiates an elimination, forming the Schiff base and releasing water with concomitant deprotonation of Lys274.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr17A hydrogen bond donor, hydrogen bond acceptor, steric role
Lys274A hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction, hydrogen bond acceptor
Lys274A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, intermediate formation, dehydration, schiff base formed

Step 9. Lys274 deprotonates the CH2 adjacent to the nitrogen, resulting in double bond rearrangement as the PLP acts as an electron sink.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr17A hydrogen bond donor, hydrogen bond acceptor, steric role
Lys274A hydrogen bond acceptor, hydrogen bond donor
Asp245A electrostatic stabiliser, hydrogen bond acceptor
Tyr144A steric role, van der waals interaction, hydrogen bond acceptor
Lys274A proton acceptor

Chemical Components

proton transfer, intermediate formation

Step 10. The PLP feeds the electrons back, the N+=C bond deprotonates Lys274.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr17A hydrogen bond donor, hydrogen bond acceptor, steric role
Lys274A hydrogen bond donor
Asp245A hydrogen bond acceptor, increase basicity
Tyr144A steric role, van der waals interaction, hydrogen bond acceptor
Lys274A proton donor

Chemical Components

proton transfer, intermediate formation

Step 11. The amine of Lys274 attacks the PLP in a nucleophilic addition reaction, the secondary amine of the attached substrate reprotonates from the bound Lys274.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr17A hydrogen bond donor, hydrogen bond acceptor, steric role
Lys274A hydrogen bond donor
Asp245A hydrogen bond acceptor, electrostatic stabiliser
Tyr144A steric role, van der waals interaction, hydrogen bond acceptor
Lys274A proton donor, nucleophile

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation

Step 12. The secondary amine that results from the initial attack initiates an elimination of the covalently bound product, resulting in 7,8-diaminononanoate and the regenerated PLP cofactor.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr17A hydrogen bond donor, steric role
Lys274A covalently attached, hydrogen bond donor
Asp245A hydrogen bond acceptor, electrostatic stabiliser
Tyr144A steric role, van der waals interaction, hydrogen bond acceptor
Lys274A electron pair donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, enzyme-substrate complex cleavage, overall product formed, intermediate collapse, intermediate terminated, native state of cofactor regenerated, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. The amine of the substrate SAM attacks the PLP cofactor in a nucleophilic addition and the bound Lys274 deprotonates the newly attached amine.

Step 2. The secondary amine that results from the initial attack initiates an elimination of the covalently bound lysine, resulting in free PLP and lysine in a neutral state.

Step 3. Lys274 deprotonates the CH adjacent to the bound amine, resulting in double bond rearrangement as the PLP acts as an electron sink.

Step 4. The PLP feeds the electrons back, resulting in the C=C attached to the aromatic ring deprotonates Lys274.

Step 5. Lys274 deprotonates water, which initiates a nucleophilic attack on the carbon of the C=N group in an addition reaction.

Step 6. The secondary amine deprotonates the attached hydroxyl group, initiating an elimination which releases S-adenosyl-4-methylthio-2-oxobutanoate.

Step 7. The amine of PMP initiates a nucleophilic attack on the carbonyl carbon of 8-amino-7-oxononanoate. The oxyanion deprotonates the newly formed secondary amine in the first step of a Schiff base formation.

Step 8. The secondary amine initiates an elimination, forming the Schiff base and releasing water with concomitant deprotonation of Lys274.

Step 9. Lys274 deprotonates the CH2 adjacent to the nitrogen, resulting in double bond rearrangement as the PLP acts as an electron sink.

Step 10. The PLP feeds the electrons back, the N+=C bond deprotonates Lys274.

Step 11. The amine of Lys274 attacks the PLP in a nucleophilic addition reaction, the secondary amine of the attached substrate reprotonates from the bound Lys274.

Step 12. The secondary amine that results from the initial attack initiates an elimination of the covalently bound product, resulting in 7,8-diaminononanoate and the regenerated PLP cofactor.

Products.

Contributors

Gemma L. Holliday, Charity Hornby