L-serine ammonia-lyase

 

L-serine ammonia-lyase is a PLP dependent enzyme that catalyses the elimination of ammonia from L-serine.

 

Reference Protein and Structure

Sequence
P09367 UniProt (4.3.1.17, 4.3.1.19) IPR001926 (Sequence Homologues) (PDB Homologues)
Biological species
Rattus norvegicus (Norway rat) Uniprot
PDB
1pwh - Rat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE (2.6 Å) PDBe PDBsum 1pwh
Catalytic CATH Domains
3.40.50.1100 CATHdb (see all for 1pwh)
Cofactors
Pyridoxal 5'-phosphate(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:4.3.1.17)

L-serine zwitterion
CHEBI:33384ChEBI
→
pyruvate
CHEBI:15361ChEBI
+
ammonium
CHEBI:28938ChEBI
Alternative enzyme names: L-hydroxyaminoacid dehydratase, L-serine deaminase, L-serine dehydratase, L-serine hydro-lyase (deaminating), Serine deaminase,

Enzyme Mechanism

Introduction

This PLP-depenedent reaction occurs via the initial elimination of water to form an enamine intermediate. This intermediate then undergoes tautomerisation to an imine form and finally the C-N bond is hydrolysed. This final step can occur spontaneously (as shown here), but it can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase.

Catalytic Residues Roles

UniProt PDB* (1pwh)
Cys339 Cys303A Acts to stabilise the PLP cofactor. hydrogen bond donor, electrostatic stabiliser
Ala258 (main-C) Ala222A (main-C) Acts to stabilise the reactive intermediates formed during the course of the reaction. hydrogen bond acceptor, electrostatic stabiliser
Lys41 Lys41A Starts the mechanism covalently attached to the PLP cofactor, during the course of the reaction it acts as a general acid/base as well as a catalytic nucleophile. covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleophile, proton acceptor, proton donor, nucleofuge, 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

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

References

  1. Yamada T et al. (2003), Biochemistry, 42, 12854-12865. Crystal Structure of Serine Dehydratase from Rat Liver†,‡. DOI:10.1021/bi035324p. PMID:14596599.
  2. Qin Z et al. (2015), Biochem Biophys Res Commun, 466, 431-437. Crystal structure and characterization of a novel L-serine ammonia-lyase from Rhizomucor miehei. DOI:10.1016/j.bbrc.2015.09.043. PMID:26367174.

Step 1. The phosphate of the PLP deprotonates the amine of L-serine, which in turn attacks the PLP cofactor in a nucleophilic addition and the bound Lys41 deprotonates the newly attached amine. This is the first step of the transaldimination reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys41A covalently attached
Cys303A hydrogen bond donor, electrostatic stabiliser
Lys41A proton acceptor, electron pair acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, 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. Final step of the transaldimination reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ala222A (main-C) hydrogen bond acceptor
Cys303A hydrogen bond donor, electrostatic stabiliser
Lys41A nucleofuge

Chemical Components

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

Step 3.

Lys41 deprotonates the CA of the covalently bound L-serine, eliminating the hydroxyl group, which deprotonates the phosphate group.

Since N1 of PLP is not protonated, the pyridine ring cannot take a quinone-like structure. Therefore, abstraction of the alpha-hydrogen from CA of serine by Lys41 would not occur. However, since the phosphate OH group can act as a general acid to donate the proton to OG of serine, abstraction of the alpha-hydrogen from CA by Lys41 occurs in a concerted fashion [PMID:14596599]. The water produced in this step is considered an intermediate, however it is not necessarily the water which is used in the final spontaneous hydrolysis.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys41A hydrogen bond acceptor
Ala222A (main-C) hydrogen bond acceptor, electrostatic stabiliser
Cys303A hydrogen bond donor, electrostatic stabiliser
Lys41A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular elimination, intermediate collapse, intermediate formation, dehydration

Step 4. Phosphate of PLP deprotonates Lys41, which attacks the PLP in a nucleophilic addition reaction, the secondary amine of the attached substrate reprotonates from the bound Lys41. First step of the transaldimination reaction. In analogy to step 1, we infer that the phosphate group acts as a base in this step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys41A hydrogen bond donor
Cys303A hydrogen bond donor, electrostatic stabiliser
Lys41A nucleophile, proton donor

Chemical Components

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

Step 5. The secondary amine that results from the initial attack initiates an elimination of the covalently bound product, resulting in 2- aminoacrylate and the regenerated PLP cofactor. Final step of the transaldimination reaction. We assume that the base in the previous step is the acid in this step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys41A covalently attached
Cys303A hydrogen bond donor, electrostatic stabiliser
Lys41A electron pair donor

Chemical Components

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

Step 6. Hydrolysis of the 2-aminoacrylate enzymatic product into pyruvate and ammonia occurs outside the enzyme active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

reaction occurs outside the enzyme, ingold: intramolecular nucleophilic addition

Step 7. Hydrolysis of the 2-aminoacrylate enzymatic product into pyruvate and ammonia occurs outside the enzyme active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

overall product formed, reaction occurs outside the enzyme, ingold: intramolecular elimination
Download: Image, Marvin File

Step 1. The phosphate of the PLP deprotonates the amine of L-serine, which in turn attacks the PLP cofactor in a nucleophilic addition and the bound Lys41 deprotonates the newly attached amine. This is the first step of the transaldimination reaction.

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. Final step of the transaldimination reaction.

Step 3.

Lys41 deprotonates the CA of the covalently bound L-serine, eliminating the hydroxyl group, which deprotonates the phosphate group.

Since N1 of PLP is not protonated, the pyridine ring cannot take a quinone-like structure. Therefore, abstraction of the alpha-hydrogen from CA of serine by Lys41 would not occur. However, since the phosphate OH group can act as a general acid to donate the proton to OG of serine, abstraction of the alpha-hydrogen from CA by Lys41 occurs in a concerted fashion [PMID:14596599]. The water produced in this step is considered an intermediate, however it is not necessarily the water which is used in the final spontaneous hydrolysis.

Step 4. Phosphate of PLP deprotonates Lys41, which attacks the PLP in a nucleophilic addition reaction, the secondary amine of the attached substrate reprotonates from the bound Lys41. First step of the transaldimination reaction. In analogy to step 1, we infer that the phosphate group acts as a base in this step.

Step 5. The secondary amine that results from the initial attack initiates an elimination of the covalently bound product, resulting in 2- aminoacrylate and the regenerated PLP cofactor. Final step of the transaldimination reaction. We assume that the base in the previous step is the acid in this step.

Step 6. Hydrolysis of the 2-aminoacrylate enzymatic product into pyruvate and ammonia occurs outside the enzyme active site.

Step 7. Hydrolysis of the 2-aminoacrylate enzymatic product into pyruvate and ammonia occurs outside the enzyme active site.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Alex Gutteridge, Craig Porter