Tyrosine 2,3-aminomutase

 

Tyrosine 2,3-aminomutase catalyses the MIO-dependent deamination of L-tyrosine to form the corresponding alpha,beta-unsaturated acid (S)-beta-tyrosine. This reaction forms part of the biosynthesis of the enediyne antitumour antibiotic C-1027.

The MIO (3,5-dihydro-5-methylidene-4H-imidazol-4-one) cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine.

 

Reference Protein and Structure

Sequence
Q8GMG0 UniProt (4.3.1.23, 5.4.3.6) IPR022314 (Sequence Homologues) (PDB Homologues)
Biological species
Streptomyces globisporus (Bacteria) Uniprot
PDB
2rjr - Substrate mimic bound to SgTAM (2.1 Å) PDBe PDBsum 2rjr
Catalytic CATH Domains
1.10.275.10 CATHdb (see all for 2rjr)
Cofactors
2-[(1s)-1-aminoethyl]-1-carboxymethyl-5-hydroxy-4-methylimidazole (1)
Click To Show Structure

Enzyme Reaction (EC:5.4.3.6)

L-tyrosine zwitterion
CHEBI:58315ChEBI
→
3-amino-3-(4-hydroxyphenyl)propanoic acid zwitterion
CHEBI:57956ChEBI
Alternative enzyme names: Tyrosine alpha,beta-mutase,

Enzyme Mechanism

Introduction

This mechanism represents the amino-MIO adduct path. Here, the amine of the substrate initiates a nucleophilic attack on the 4-ene carbon of the cofactor. Tyr63 acts as a general acid/base which initiates the elimnation that results in the aminated cofactor and coumarate. Collapse of the oxyanion results in a nucleophilic attack on the coumarate intermediate in an addition reaction forming the final product and concomitant deprotonation of Tyr63.

Catalytic Residues Roles

UniProt PDB* (2rjr)
Tyr63 Tyr63A Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Gly70 (main-N) Gly70A (main-N) Helps stabilise Tyr63 in the negative state. hydrogen bond donor, electrostatic stabiliser
*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, cofactor used, enzyme-substrate complex formation, intermediate formation, overall reactant used, bimolecular elimination, intermediate collapse, enzyme-substrate complex cleavage, unimolecular elimination by the conjugate base, native state of cofactor regenerated, native state of enzyme regenerated, intermediate terminated, overall product formed

References

  1. Christianson CV et al. (2007), Biochemistry, 46, 7205-7214. The Structure ofl-Tyrosine 2,3-Aminomutase from the C-1027 Enediyne Antitumor Antibiotic Biosynthetic Pathway†,‡. DOI:10.1021/bi7003685. PMID:17516659.
  2. Christianson CV et al. (2007), J Am Chem Soc, 129, 15744-15745. The Mechanism of MIO-Based Aminomutases in β-Amino Acid Biosynthesis. DOI:10.1021/ja0762689. PMID:18052279.

Step 1. The amine of the substrate tyrosine initiates a nucleophilic attack upon the 4-ene carbon of the MIO cofator, resulting in double bond rearrangement and the formation of an oxyanion.

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Catalytic Residues Roles

Residue Roles
Gly70A (main-N) hydrogen bond donor
Tyr63A hydrogen bond acceptor
Gly70A (main-N) electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic addition, cofactor used, enzyme-substrate complex formation, intermediate formation, overall reactant used

Step 2. Tyr63 deprotonates the covalently bound tyrosine substrate initiating an elimination that results in the aminated cofactor and coumarate.

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Catalytic Residues Roles

Residue Roles
Tyr63A hydrogen bond acceptor
Gly70A (main-N) hydrogen bond donor
Gly70A (main-N) electrostatic stabiliser
Tyr63A proton acceptor

Chemical Components

ingold: bimolecular elimination, intermediate collapse, intermediate formation, enzyme-substrate complex cleavage

Step 3. The oxyanion collapses, eliminating the ammonia group, which initiates a nucleophilic attack on the coumarate intermediate in an addition reaction with concomitant deprotonation of Tyr63

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Catalytic Residues Roles

Residue Roles
Gly70A (main-N) hydrogen bond donor
Tyr63A hydrogen bond donor, hydrogen bond acceptor
Gly70A (main-N) electrostatic stabiliser
Tyr63A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, ingold: bimolecular nucleophilic addition, native state of cofactor regenerated, enzyme-substrate complex cleavage, native state of enzyme regenerated, intermediate terminated, overall product formed
Download: Image, Marvin File

Step 1. The amine of the substrate tyrosine initiates a nucleophilic attack upon the 4-ene carbon of the MIO cofator, resulting in double bond rearrangement and the formation of an oxyanion.

Step 2. Tyr63 deprotonates the covalently bound tyrosine substrate initiating an elimination that results in the aminated cofactor and coumarate.

Step 3. The oxyanion collapses, eliminating the ammonia group, which initiates a nucleophilic attack on the coumarate intermediate in an addition reaction with concomitant deprotonation of Tyr63

Products.

Introduction

In this alternative mechanism the aromatic ring of the substrate initiates nucleophilic attack on the 4-ene group of the cofactor, resulting in a carbocation intermediate in the aromatic ring and an oxyanion intermediate in the cofactor. Tyr63 acts as a general acid/base catalyst resulting in the carbocation being neutralized which leads to the elimination of ammonia and collapse of the substrate cofactor complex. The re-addition of ammnoia on to the substare leads to the formation of the final product along with the concomitant deprotonation of Tyr63.

Catalytic Residues Roles

UniProt PDB* (2rjr)
Tyr63 Tyr63A Acts as a general acid/base. hydrogen bond acceptor, proton acceptor, proton donor
Gly70 (main-N) Gly70A (main-N) Helps stabilise Tyr63 in the negative state. hydrogen bond donor, electrostatic stabiliser
*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

michael addition, overall reactant used, cofactor used, intermediate formation, enzyme-substrate complex formation, aromatic bimolecular electrophilic addition, proton transfer, aromatic intramolecular elimination, native state of cofactor regenerated, intermediate terminated, enzyme-substrate complex cleavage, overall product formed, bimolecular nucleophilic addition, native state of enzyme regenerated

References

  1. Christianson CV et al. (2007), J Am Chem Soc, 129, 15744-15745. The Mechanism of MIO-Based Aminomutases in β-Amino Acid Biosynthesis. DOI:10.1021/ja0762689. PMID:18052279.

Step 1. The aromatic ring of the substrate tyrosine initiates a nucleophilic attack upon the 4-ene carbon of the MIO cofator, resulting in double bond rearrangement and the formation of an oxyanion on the cofactor and the formation of a carbocation in the aromatic ring.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly70A (main-N) electrostatic stabiliser
Gly70A (main-N) hydrogen bond donor
Tyr63A hydrogen bond acceptor

Chemical Components

michael addition, overall reactant used, cofactor used, intermediate formation, enzyme-substrate complex formation, ingold: aromatic bimolecular electrophilic addition

Step 2. Tyr63 deprotonates the substrate tyrosine, resulting in a C=C bond being formed and the neutralization of the carbocation.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly70A (main-N) electrostatic stabiliser
Tyr63A hydrogen bond acceptor
Gly70A (main-N) hydrogen bond donor
Tyr63A proton acceptor

Chemical Components

proton transfer

Step 3. The covalent bond between the cofactor and substrate is broken leading to the rearrangement of the C=C bonds which results in ammonia being eliminated.

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Catalytic Residues Roles

Residue Roles
Gly70A (main-N) electrostatic stabiliser

Chemical Components

ingold: aromatic intramolecular elimination, native state of cofactor regenerated, intermediate terminated, enzyme-substrate complex cleavage

Step 4. The ammonia attacks the newly formed C=C double bond of the substrate in an addition reaction with concomitant deprotonation of Tyr63.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly70A (main-N) electrostatic stabiliser, hydrogen bond donor
Tyr63A hydrogen bond acceptor, proton donor

Chemical Components

overall product formed, ingold: bimolecular nucleophilic addition, proton transfer, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. The aromatic ring of the substrate tyrosine initiates a nucleophilic attack upon the 4-ene carbon of the MIO cofator, resulting in double bond rearrangement and the formation of an oxyanion on the cofactor and the formation of a carbocation in the aromatic ring.

Step 2. Tyr63 deprotonates the substrate tyrosine, resulting in a C=C bond being formed and the neutralization of the carbocation.

Step 3. The covalent bond between the cofactor and substrate is broken leading to the rearrangement of the C=C bonds which results in ammonia being eliminated.

Step 4. The ammonia attacks the newly formed C=C double bond of the substrate in an addition reaction with concomitant deprotonation of Tyr63.

Products.

Contributors

Gemma L. Holliday, James Willey