Serine racemase

 

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].

 

Reference Protein and Structure

Sequence
O59791 UniProt (4.3.1.17, 4.3.1.18, 5.1.1.18) IPR001926 (Sequence Homologues) (PDB Homologues)
Biological species
Schizosaccharomyces pombe 972h- (Fission yeast) Uniprot
PDB
2zr8 - Crystal Structure of Modified Serine Racemase complexed with Serine (2.2 Å) PDBe PDBsum 2zr8
Catalytic CATH Domains
3.40.50.1100 CATHdb (see all for 2zr8)
Cofactors
Magnesium(2+) (1), Pyridoxal 5'-phosphate(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:5.1.1.18)

L-serine zwitterion
CHEBI:33384ChEBI
→
D-serine zwitterion
CHEBI:35247ChEBI
Alternative enzyme names: SRR,

Enzyme Mechanism

Introduction

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. Ser82 returns a proton to the serine C-alpha position from the alternative face of the molecule, reversing the previous stereochemistry. The deprotonated Lys57 acts as a nucleophile towards the PDD-serine complex, forming a precursor to the regeneration of the internal aldimine. The tetrahedral intermediate collapses releasing L/D-serine, inverted at the c-alpha relative to the starting material, and the internal aldimine is regenerated.

Catalytic Residues Roles

UniProt PDB* (2zr8)
Glu208, Gly212 (main-C), Asp214 Glu208A, Gly212A (main-C), Asp214A Forms part of the magnesium binding site. metal ligand
Ser308 Ser308A Acts to stabilise the reactive intermediates and transition states during the course of the reaction. attractive charge-charge interaction, hydrogen bond acceptor, electrostatic stabiliser
Ser82 Ser82A Suggested to act as a general acid/base during the course of the reaction. proton acceptor, hydrogen bond acceptor, electrostatic stabiliser, proton donor
Lys57 Lys57A Lys57 is covalently attached to the PLP cofactor in the ground state of the reaction. It is thought to act as a general acid/base during the course of the reaction. covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleophile, proton acceptor, proton donor, nucleofuge, activator, 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, intermediate formation, overall reactant used, schiff base formed, cofactor used, elimination (not covered by the Ingold mechanisms), intermediate collapse, enzyme-substrate complex cleavage, enzyme-substrate complex formation, overall product formed, native state of enzyme regenerated, native state of cofactor regenerated

References

  1. Gogami Y et al. (2010), Chem Biodivers, 7, 1579-1590. Site-Directed Mutagenesis of Rice Serine Racemase: Evidence That Glu219 and Asp225 Mediate the Effects of Mg2+ on the Activity. DOI:10.1002/cbdv.200900257. PMID:20564571.
  2. Nitoker N et al. (2015), Biochemistry, 54, 516-527. Understanding the reaction mechanism and intermediate stabilization in mammalian serine racemase using multiscale quantum-classical simulations. DOI:10.1021/bi500984m. PMID:25493718.
  3. Goto M et al. (2009), J Biol Chem, 284, 25944-25952. Crystal Structure of a Homolog of Mammalian Serine Racemase from Schizosaccharomyces pombe. DOI:10.1074/jbc.m109.010470. PMID:19640845.
  4. Yamauchi T et al. (2009), J Biochem, 145, 421-424. Serine Racemase with Catalytically Active Lysinoalanyl Residue*. DOI:10.1093/jb/mvp010. PMID:19155267.

Step 1. The neutral amine group of L-serine attacks the imine functionality of the pyridoxal-5-phosphate cofactor, forming a Schiff base precursor.

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Catalytic Residues Roles

Residue Roles
Ser308A attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor
Lys57A covalently attached, activator
Ser82A hydrogen bond acceptor
Glu208A metal ligand
Gly212A (main-C) metal ligand
Asp214A metal ligand
Lys57A proton acceptor, electron pair acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used, schiff base formed, cofactor used

Step 2. The tetrahedral intermediate collapses, generating the external aldimine, PDD-substrate complex.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser308A attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor
Lys57A activator
Ser82A hydrogen bond acceptor
Glu208A metal ligand
Gly212A (main-C) metal ligand
Asp214A metal ligand
Lys57A nucleofuge

Chemical Components

elimination (not covered by the Ingold mechanisms), intermediate formation, intermediate collapse, enzyme-substrate complex cleavage, schiff base formed, cofactor used

Step 3. Either Lys57 or Ser82 acts as a general base towards the C-alpha of the covalently bound serine, forming a planar sterocentre [PMID:19640845]. Lys57 shown here in analogy to other PLP-dependent enzymes.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser82A electrostatic stabiliser
Ser308A electrostatic stabiliser
Glu208A metal ligand
Gly212A (main-C) metal ligand
Asp214A metal ligand
Lys57A proton acceptor

Chemical Components

proton transfer, intermediate formation

Step 4. Either Lys57 or Ser82 returns a proton to the serine C-alpha position from the alternative face of the molecule, reversing the previous stereochemistry. Ser82 shown as this reaction results in a different steroisomer to the original molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser308A attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor
Lys57A activator, hydrogen bond donor
Ser82A hydrogen bond acceptor
Glu208A metal ligand
Gly212A (main-C) metal ligand
Asp214A metal ligand
Ser82A proton donor

Chemical Components

proton transfer, intermediate formation

Step 5. Ser82 abstracts a proton from Lys57. The deprotonated Lys57 acts as a nucleophile towards the PLP-serine complex, forming a precursor to the regeneration of the internal aldimine.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser308A attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor
Lys57A activator, hydrogen bond acceptor, covalently attached
Ser82A hydrogen bond acceptor
Glu208A metal ligand
Gly212A (main-C) metal ligand
Asp214A metal ligand
Lys57A nucleophile, proton donor
Ser82A proton acceptor

Chemical Components

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

Step 6. The tetrahedral intermediate collapses releasing L/D-serine, inverted at the c-alpha relative to the starting material, and the internal aldimine is regenerated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser308A attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor
Lys57A covalently attached, activator, hydrogen bond acceptor
Ser82A hydrogen bond acceptor
Glu208A metal ligand
Gly212A (main-C) metal ligand
Asp214A metal ligand
Lys57A electron pair donor

Chemical Components

elimination (not covered by the Ingold mechanisms), intermediate collapse, cofactor used, overall product formed, native state of enzyme regenerated, native state of cofactor regenerated
Download: Image, Marvin File

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. Either Lys57 or Ser82 acts as a general base towards the C-alpha of the covalently bound serine, forming a planar sterocentre [PMID:19640845]. Lys57 shown here in analogy to other PLP-dependent enzymes.

Step 4. Either Lys57 or Ser82 returns a proton to the serine C-alpha position from the alternative face of the molecule, reversing the previous stereochemistry. Ser82 shown as this reaction results in a different steroisomer to the original molecule.

Step 5. Ser82 abstracts a proton from Lys57. The deprotonated Lys57 acts as a nucleophile towards the PLP-serine complex, forming a precursor to the regeneration of the internal aldimine.

Step 6. The tetrahedral intermediate collapses releasing L/D-serine, inverted at the c-alpha relative to the starting material, and the internal aldimine is regenerated.

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday