Aspartate Ammonia Lyase

 

Aspartate Ammonia Lyase is one of the three ammonia lyases that belong to aspartate/fumarase superfamily. It catalyses the reversible reaction of L-aspartate to make ammonia and fumarate and is important in microbial nitrogen metabolism. It is also an industrial precursor for the synthesis of food additives and artificial sweeteners.

 

Reference Protein and Structure

Sequence
Q9LCC6 UniProt (4.3.1.1) IPR004708 (Sequence Homologues) (PDB Homologues)
Biological species
Bacillus sp. YM55-1 (Bacteria) Uniprot
PDB
3r6v - Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate (2.6 Å) PDBe PDBsum 3r6v
Catalytic CATH Domains
1.10.275.10 CATHdb 1.20.200.10 CATHdb (see all for 3r6v)
Click To Show Structure

Enzyme Reaction (EC:4.3.1.1)

L-aspartate(1-)
CHEBI:29991ChEBI
→
fumarate(2-)
CHEBI:29806ChEBI
+
ammonium
CHEBI:28938ChEBI
Alternative enzyme names: L-aspartase, Aspartase, Fumaric aminase, L-aspartate ammonia-lyase,

Enzyme Mechanism

Introduction

Aspartate ammonia lyase (Asp) catalyses the reversible reaction of L-aspartate to give fumarate and ammonia. The first and the rate limiting step is the deprotonation of L-aspartate by the catalytic base Ser318 followed by the displacement of the ammonia through the rearrangement of the double bond formed in the enediolate intermediate to form fumarate and ammonia as a product.

Catalytic Residues Roles

UniProt PDB* (3r6v)
His188 His188A Protonates the leaving ammonia. increase basicity, hydrogen bond donor, proton donor
Ser318 Ser318C Ser318 acts as the catalytic base. proton donor
Thr187, Lys324, Asn142, Ser140, Thr141, Ser319, Thr101 Thr187A, Lys324C, Asn142B, Ser140B, Thr141B, Ser319C, Thr101B Form an extensive hydrogen bond network that stabilises the transition state and intermediates. hydrogen bond 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

rate-determining step, proton transfer, overall product formed, unimolecular elimination by the conjugate base

References

  1. Zhang J et al. (2014), J Mol Graph Model, 51, 113-119. A QM/MM study of the catalytic mechanism of aspartate ammonia lyase. DOI:10.1016/j.jmgm.2014.05.003. PMID:24875395.
  2. de Villiers M et al. (2012), ACS Chem Biol, 7, 1618-1628. Catalytic Mechanisms and Biocatalytic Applications of Aspartate and Methylaspartate Ammonia Lyases. DOI:10.1021/cb3002792. PMID:22834890.
  3. Fibriansah G et al. (2011), Biochemistry, 50, 6053-6062. Structural basis for the catalytic mechanism of aspartate ammonia lyase. DOI:10.1021/bi200497y. PMID:21661762.
  4. Fibriansah G et al. (2011),Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate. DOI:10.2210/pdb3r6v/pdb.
  5. Puthan Veetil V et al. (2009), FEBS J, 276, 2994-3007. Site-directed mutagenesis, kinetic and inhibition studies of aspartate ammonia lyase from Bacillus sp. YM55-1. DOI:10.1111/j.1742-4658.2009.07015.x. PMID:19490103.

Step 1. Ser318 acts as a catalytic base and deprotonates the Cβ proton of L-aspartate substrate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser318C proton donor
His188A increase basicity, hydrogen bond donor
Thr187A hydrogen bond donor
Asn142B hydrogen bond donor
Thr101B hydrogen bond donor
Lys324C hydrogen bond donor
Thr141B hydrogen bond donor
Ser319C hydrogen bond donor
Ser140B hydrogen bond donor

Chemical Components

rate-determining step, proton transfer

Step 2. Rearrangement of double bond displaces the NH3+. His188 loses a proton to the leaving ammonia.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His188A proton donor, hydrogen bond donor
Thr187A hydrogen bond donor
Asn142B hydrogen bond donor
Thr101B hydrogen bond donor
Lys324C hydrogen bond donor
Thr141B hydrogen bond donor
Ser319C hydrogen bond donor
Ser140B hydrogen bond donor

Chemical Components

overall product formed, ingold: unimolecular elimination by the conjugate base, proton transfer
Download: Image, Marvin File

Step 1. Ser318 acts as a catalytic base and deprotonates the Cβ proton of L-aspartate substrate.

Step 2. Rearrangement of double bond displaces the NH3+. His188 loses a proton to the leaving ammonia.

Products.

Contributors

Yordanos Abeje, Antonio Ribeiro