Cofactors

Pyridoxal 5'-phosphate.

Reaction Mechanism

L-serine ammonia-lyase By Reference

serine racemase (SRR) catalyses the PLP-dependent synthesis of D-serine from L-serine (and vice versa. SRR also has dehydratase activity towards both L-serine and D-serine, resulting in pyruvate and ammonia. It is allosterically activated by ATP, by magnesium, and possibly also by other divalent metal cations. The magnesium ion present in the crystal structure is thought to be essential for the structural integrity of the enzymes, and not directly involved in catalysis [PMID:20564571].




• Summary
• Step 1
• Step 2
• Step 3
• Step 4
• Step 5
• Step 6
• Step 7
• Step 8
• Products

The neutral amine group of L-serine attacks the imine functionality of the pyridoxal-5-phosphate cofactor, forming a Schiff base precursor. The tetrahedral intermediate collapses, generating the external aldimine, PDD-substrate complex. Lys57 acts as a general base towards the C-alpha of the covalently bound serine, forming a planar sterocentre [PMID:19640845]. Beta-elimination of water from the carbaion can occur to form an amino-acrylate intermediate. This undergoes non-enzymatic hydrolysis to form water, ammonia and a lysino-alanine modified PLP cofactor which is still capable of isomerase activity [PMID:19155267, PMID:19640845]. Lys57 then acts as a nucleophile to regenerate the cofactor and the final enzymatic product. It is thought that the final hydrolysis occurs outside of the enzyme active site.

Catalytic Residues

AA	Uniprot	Uniprot Resid	PDB	PDB Resid
Ser	O59791	82	2zr8	82
Lys	O59791	57	2zr8	57
Gly	O59791	212	2zr8	212
Asp	O59791	214	2zr8	214
Ser	O59791	308	2zr8	308
Glu	O59791	208	2zr8	208

Step Components

native state of cofactor regenerated, hydrolysis, bimolecular nucleophilic addition, enzyme-substrate complex formation, proton transfer, native state of enzyme regenerated, elimination (not covered by the Ingold mechanisms), enzyme-substrate complex cleavage, reaction occurs outside the enzyme, overall reactant used, unimolecular elimination by the conjugate base, schiff base formed, overall product formed



Step 1.

The neutral amine group of L-serine attacks the imine functionality of the pyridoxal-5-phosphate cofactor, forming a Schiff base precursor.



Step 2.

The tetrahedral intermediate collapses, generating the external aldimine, PDD-substrate complex.



Step 3.

Lys57 acts as a general base towards the C-alpha of the covalently bound serine, forming a planar sterocentre [PMID:19640845].



Step 4.

Beta-elimination of water from the carbaion can occur to form an amino-acrylate intermediate.



Step 5.

Lys57 acts as a nucleophile towards the PLP-serine complex, forming a precursor to the regeneration of the internal aldimine.



Step 6.

Lys57 eliminates the enzymatic product to generate the reactive cofactor species which is capable of performing a new catalytic cycle.



Step 7.

Hydrolysis of the 2-aminoacrylate enzymatic product into pyruvate and ammonia is thought to occur outside the enzyme active site.



Step 8.

Final step of the non-enzymatic hydrolysis.



Products.

The products of the reaction.

View Reaction Mechanisms in M-CSA

Reaction Parameters

• Kinetic Parameters

  Organism	KM Value [mM]	Substrate	Comment
  Saccharomyces cerevisiae	0.012	D-serine	pH 8, 30°C, mutant Y203D
  Dictyostelium discoideum	14	D-serine	pH 8.5, 30°C

• Temperature

  There are no reaction parameters information for this Enzyme.

• pH

  Organism	pH Range	Comment
  Klebsiella pneumoniae	6 - 8.5	pH 6.0: about 30% of maximal activity, pH 8.5: about 60% of maximal activity
  Escherichia coli	6.5 - 9	pH 6.5: about 30% of maximal activity, pH 9.0: about 60% of maximal activity
  Gallus gallus	6.5 - 11.5	in the range of pH 6.5-11.5 the enzyme has an activity between 50 and 100% with an maximum at pH 9

Associated Proteins

Citations

• Structural basis of the inhibition of cystathionine γ-lyase from Toxoplasma gondii by propargylglycine and cysteine.
• Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus.
• Quantitative Physiology and Proteome Adaptations of Bifidobacterium breve NRBB57 at Near-Zero Growth Rates.
• Use of Trichoderma culture filtrates as a sustainable approach to mitigate early blight disease of tomato and their influence on plant biomarkers and antioxidants production.
• Phenylalanine Ammonia-Lyase: A Key Gene for Color Discrimination of Edible Mushroom Flammulina velutipes.
• Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato.
• Faecal microbiota transplant restores intestinal barrier function and augments ammonia metabolism in patients with cirrhosis: a randomised single-blind placebo-controlled trial
• Variation of growth and transcriptome responses to arbuscular mycorrhizal symbiosis in different foxtail millet lines.
• Transcriptomics reveals the effect of ammonia nitrogen concentration on Pseudomonas stutzeri F2 assimilation and the analysis of amtB function.
• Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance against Diaporthe caulivora.
• Sulfur-Element containing metabolic pathways in human health and crosstalk with the microbiome.