Scyllo-inosamine-4-phosphate amidinotransferase

 

Inosamine-phosphate amidinotransferase catalyses two reactions in the biosynthesis of antibiotics in the streptomycin family. The structure of this enzyme is similar to that of glycine amidinotransferase, being an alpha-beta 5-propeller and the active site residues are in the same spatial positions.

 

Reference Protein and Structure

Sequence
P08078 UniProt (2.1.4.2) IPR033195 (Sequence Homologues) (PDB Homologues)
Biological species
Streptomyces griseus (Bacteria) Uniprot
PDB
1bwd - INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE STRB1 FROM STREPTOMYCES GRISEUS (3.1 Å) PDBe PDBsum 1bwd
Catalytic CATH Domains
3.75.10.10 CATHdb (see all for 1bwd)

Enzyme Reaction (EC:2.1.4.2)

L-argininium(1+)
CHEBI:32682ChEBI
+
1-ammonio-1-deoxy-scyllo-inositol 4-phosphate(1-)
CHEBI:58325ChEBI
→
1-guanidino-1-deoxy-scyllo-inositol 4-phosphate(1-)
CHEBI:57656ChEBI
+
L-ornithinium(1+)
CHEBI:46911ChEBI
Alternative enzyme names: L-arginine:inosamine phosphate amidinotransferase, L-arginine:inosamine-P-amidinotransferase, Inosamine-P amidinotransferase, Inosamine-phosphate amidinotransferase,

Enzyme Mechanism

Introduction

The proposed transamidination starts with the binding of L-arginine and the subsequent nucleophilic attack of the thiolate anion of Cys332 on the positively polarized carbon atom of the guanidino group. As the tetrahedral transition state decays, a covalent cysteine−amidino intermediate and l-ornithine are formed. The binding of the amidino acceptor scyllo-inosamine 4-phosphate, the nucleophilic attack on the planar isothiourea group, and the liberation of the reaction product are the final steps of the reaction cycle.

Catalytic Residues Roles

UniProt PDB* (1bwd)
Asp179 Asp179A Involved in stabilising the imidazole ring of the general acid/base histidine (His227). modifies pKa
His227 His227A Acts as a general acid/base. proton shuttle (general acid/base)
Asp229 Asp229A Acts as a general acid/base in the activation of the nucleophilic cysteine residue. Part of the catalytic Cys-Asp-His triad. proton shuttle (general acid/base)
His331 His331A Acts as a general acid/base in the catalytic Cys-Asp-His triad. proton shuttle (general acid/base)
Cys332 Cys332A Acts as the catalytic nucleophile, it is activated as part of a Cys-Asp-His triad. covalent catalysis, proton shuttle (general acid/base)
Asp108 Asp108A Helps to stabilise the isothiourea group. electrostatic stabiliser
Glu9 Glu9A Increases the pKa value of His331, enabling it to act as the terminal acid/base in the activation of the cysteine nucleophile. modifies pKa
Asn286 Asn286A Involved in activating the nucleophilic cysteine residue. modifies pKa
*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

References

  1. Fritsche E et al. (1998), Biochemistry, 37, 17664-17672. Crystal Structure ofl-Arginine:Inosamine-Phosphate Amidinotransferase StrB1 fromStreptomycesgriseus:  An Enzyme Involved in Streptomycin Biosynthesis‡. DOI:10.1021/bi981949p. PMID:9922132.

Step 1.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu9A modifies pKa
Asp108A electrostatic stabiliser
His227A proton shuttle (general acid/base)
Asp229A proton shuttle (general acid/base)
Asn286A modifies pKa
His331A proton shuttle (general acid/base)
Cys332A proton shuttle (general acid/base), covalent catalysis
Asp179A modifies pKa

Chemical Components

Step 1.

Contributors

Nozomi Nagano, Gemma L. Holliday, Craig Porter