Cystathionine beta-synthase

 

Mammalian cystathionine beta-synthase (CBS) is a heme protein that catalyses the conversion of L-serine and L-homocysteine (L-Hcys) to give cystathionine in the first step in the transulfuration pathway. CBS is a member of the beta-family (Fold-type II) of pyridoxal 5'-phosphate (PLP) enzymes. These catalyse PLP-dependent, beta-replacement reactions in which the electronegative substituent in the beta-position of the amino acid substrate (in the case of CBS, the -OH group of L-Ser), is replaced by a sulphur-containing nucleophile (L-Hcys thiol group). Human CBS (hCBS) has three domains - the N-terminal domain where heme, which is not essential for catalysis and the function of which is still uncertain, is bound; the core catalytic dimeric domain where PLP is bound; and the C-terminal domain where the allosteric activator of the enzyme, S-adenosyl-L-methionine (AdoMet), is bound.

 

Reference Protein and Structure

Sequence
P35520 UniProt (4.2.1.22) IPR005857 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1m54 - CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS (2.9 Å) PDBe PDBsum 1m54
Catalytic CATH Domains
3.40.50.1100 CATHdb (see all for 1m54)
Cofactors
Pyridoxal 5'-phosphate(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.22)

L-serine zwitterion
CHEBI:33384ChEBI
+
L-homocysteine zwitterion
CHEBI:58199ChEBI
→
L-cystathionine dizwitterion
CHEBI:58161ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: Beta-thionase, Cysteine synthase, Methylcysteine synthase, Serine sulfhydrase, Serine sulfhydrylase, L-serine hydro-lyase (adding homocysteine),

Enzyme Mechanism

Introduction

On addition of the first substrate, L-Ser, a transaldimination reaction takes place. The internal aldimine, formed by PLP bound to the enzyme via the amino acid residue Lys119, is converted into an external aldimine by replacing Lys with L-Ser. Following the binding of the second substrate, L-Hcys, to the enzyme the alpha-proton and beta-hydroxide of the external aldimine are abstracted and eliminated to form water and the alpha-aminoacrylate intermediate. The aminoacrylate intermediate undergoes nucleophilic addition by the thiolate of L-Hcys to form a quinonoid intermediate. A second transaldimination occurs where the resting enzyme is regenerated and the product (cystathionine) is released.

Catalytic Residues Roles

UniProt PDB* (1m54)
Lys119 Lys119(76)A Cofactor PLP is held in the active site as an internal aldimine via a Schiff base linkage formed with Lys119. covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay, 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, overall reactant used, intermediate formation, intramolecular elimination, schiff base formed, intermediate terminated, bimolecular elimination, proton transfer, proton relay, native state of cofactor regenerated, native state of enzyme regenerated, overall product formed

References

  1. Taoka S et al. (2002), Biochemistry, 41, 10454-10461. Human Cystathionine β-Synthase Is a Heme Sensor Protein. Evidence That the Redox Sensor Is Heme and Not the Vicinal Cysteines in the CXXC Motif Seen in the Crystal Structure of the Truncated Enzyme†,⊥. DOI:10.1021/bi026052d. PMID:12173932.
  2. Tu Y et al. (2018), Biochemistry, 57, 3134-3145. Crystal Structures of Cystathionine β-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. DOI:10.1021/acs.biochem.8b00092. PMID:29630349.

Step 1. The nitrogen of the substrate serine performs a nucleophillic attack upon the aldimine bond forming a tetrahedral intermediate.

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Catalytic Residues Roles

Residue Roles
Lys119(76)A covalently attached
Lys119(76)A electron pair acceptor

Chemical Components

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

Step 2. Lys119 is eliminated and a new aldimine bond is formed between the serine and PLP.

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Catalytic Residues Roles

Residue Roles
Lys119(76)A nucleofuge

Chemical Components

ingold: intramolecular elimination, schiff base formed, intermediate terminated

Step 3. Lys119 accepts a proton from the serine alpha carbon this leads to water being eliminated from the beta carbon forming an aminoacrylate intermediate.

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Catalytic Residues Roles

Residue Roles
Lys119(76)A proton acceptor

Chemical Components

ingold: bimolecular elimination, proton transfer

Step 4. The thiol group of the cysteine performs a nucleophilic attack on the C=C bond of the aminoacrylate forming a quinonoid intermediate, with Lys119 acting as a proton relay.

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Catalytic Residues Roles

Residue Roles
Lys119(76)A proton relay
Lys119(76)A proton acceptor, proton donor

Chemical Components

ingold: bimolecular nucleophilic addition, proton relay

Step 5. Lys119 performs a nucleophilic attack on the aldimine bond in a second transaldimination reaction.

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Catalytic Residues Roles

Residue Roles
Lys119(76)A covalently attached, nucleophile

Chemical Components

ingold: bimolecular nucleophilic addition, intermediate formation

Step 6. The product is eliminated from PLP, regenerating the enzyme in its native state.

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Catalytic Residues Roles

Residue Roles
Lys119(76)A covalently attached, electron pair donor

Chemical Components

ingold: intramolecular elimination, intermediate terminated, native state of cofactor regenerated, native state of enzyme regenerated, overall product formed
Download: Image, Marvin File

Step 1. The nitrogen of the substrate serine performs a nucleophillic attack upon the aldimine bond forming a tetrahedral intermediate.

Step 2. Lys119 is eliminated and a new aldimine bond is formed between the serine and PLP.

Step 3. Lys119 accepts a proton from the serine alpha carbon this leads to water being eliminated from the beta carbon forming an aminoacrylate intermediate.

Step 4. The thiol group of the cysteine performs a nucleophilic attack on the C=C bond of the aminoacrylate forming a quinonoid intermediate, with Lys119 acting as a proton relay.

Step 5. Lys119 performs a nucleophilic attack on the aldimine bond in a second transaldimination reaction.

Step 6. The product is eliminated from PLP, regenerating the enzyme in its native state.

Products.

Contributors

Gemma L. Holliday, James Willey