Phosphoribosylaminoimidazolecarboxamide formyltransferase

 

The enzyme AITC is bifunctional being involved in the production of IMP, the final product of the de novo purine synthesis pathway.. The catalytic centre described here catalyses the first step in AIRC activity, the formylation of AICAR to form 5-formyl AICAR which can then be cyclised by the second catalytic centre. The enzyme shows a high degree of sequence conservation among organisms from E.coli to man, but does not show homology to other formyl transferases, suggesting that the bifunctionality has evolved from one gene rather than two.

 

Reference Protein and Structure

Sequence
P31939 UniProt (2.1.2.3, 3.5.4.10) IPR002695 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1p4r - Crystal Structure of Human ATIC in complex with folate-based inhibitor BW1540U88UD (2.55 Å) PDBe PDBsum 1p4r
Catalytic CATH Domains
3.40.140.20 CATHdb (see all for 1p4r)
Click To Show Structure

Enzyme Reaction (EC:2.1.2.3)

5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide(2-)
CHEBI:58475ChEBI
+
10-formyltetrahydrofolate(2-)
CHEBI:57454ChEBI
→
(6S)-5,6,7,8-tetrahydrofolate(2-)
CHEBI:57453ChEBI
+
5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide(2-)
CHEBI:58467ChEBI
Alternative enzyme names: 10-formyltetrahydrofolate:5'-phosphoribosyl-5-amino-4-imidazolecarboxamide formyltransferase, 5'-phosphoribosyl-5-amino-4-imidazolecarboxamide formyltransferase, 5-amino-1-ribosyl-4-imidazolecarboxamide 5'-phosphate transformylase, 5-amino-4-imidazolecarboxamide ribonucleotide transformylase, 5-amino-4-imidazolecarboxamide ribotide transformylase, AICAR formyltransferase, AICAR transformylase, Aminoimidazolecarboxamide ribonucleotide transformylase,

Enzyme Mechanism

Introduction

The cofactor which supplies the formyl group is N10-formyl-tetrahydrofolate (10-f-THF). During the reaction nucleophilic attack by the amino group of AICAR, facilitated by deprotonation by His 267, forms a tetrahedral intermediate, stabilised by Lys 266 and Asn 431. This collapses following protonation of the cofactor by Lys 266 to release the product. His 267 is activated towards its role as a general base by Asn 431 and His 593.

Catalytic Residues Roles

UniProt PDB* (1p4r)
Lys266 Lys266A Stabilises transition state by forming electrostatic interactions with the negatively charged oxygen of the tetrahedral intermediate, then protonates the THF cofactor to allow it to act as a leaving group for the reaction so that the tetrahedral intermediate collapses. proton acceptor, proton relay, electrostatic stabiliser, proton donor
His267 His267A Deprotonates AICAR to allow its amino group to attack THF as a nucleophile, forming the tetrahedral intermediate that collapses to the product. proton relay, proton acceptor, electrostatic stabiliser, proton donor
His592 His592B Acts as a primer by modifying the pKa of His 267 so that it can act as a general acid base during the reaction. proton acceptor, proton donor, proton relay, electrostatic stabiliser, modifies pKa
Asn431 Asn431B Stabilises tetrahedral intermediate through hydrogen bonding, and also acts to modify the pKa of His 267 to allow it to function as a general acid base. modifies pKa, 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

proton relay, proton transfer, overall reactant used, bimolecular nucleophilic addition, intermediate collapse, native state of enzyme regenerated, overall product formed, elimination (not covered by the Ingold mechanisms)

References

  1. Shim JH et al. (2001), J Am Chem Soc, 123, 4687-4696. Evaluation of the Catalytic Mechanism of AICAR Transformylase by pH-Dependent Kinetics, Mutagenesis, and Quantum Chemical Calculations. DOI:10.1021/ja010014k. PMID:11457277.
  2. Cheong CG et al. (2004), J Biol Chem, 279, 18034-18045. Crystal Structures of Human Bifunctional Enzyme Aminoimidazole-4-carboxamide Ribonucleotide Transformylase/IMP Cyclohydrolase in Complex with Potent Sulfonyl-containing Antifolates. DOI:10.1074/jbc.m313691200. PMID:14966129.
  3. Wolan DW et al. (2002), Biochemistry, 41, 15505-15513. Structural Insights into the Avian AICAR Transformylase Mechanism†. DOI:10.1021/bi020505x. PMID:12501179.

Step 1. Solvent deprotoantes His592 which triggers the subsequent deprotonation of His267 and the substrate amine group. The amine then attacks the aldehyde group of 10-f-THF.

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Catalytic Residues Roles

Residue Roles
Asn431B electrostatic stabiliser
Lys266A electrostatic stabiliser
His592B electrostatic stabiliser
His267A electrostatic stabiliser
His592B modifies pKa
Asn431B modifies pKa
His267A proton donor, proton acceptor
His592B proton donor, proton acceptor, proton relay
His267A proton relay

Chemical Components

proton relay, proton transfer, overall reactant used, ingold: bimolecular nucleophilic addition

Step 2. The tetrahedral intermediate collapses to form the product and the cofactor is protonated by Lys266. The native state of the enzyme is regenerated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His267A proton relay
His592B proton relay
Asn431B electrostatic stabiliser, modifies pKa
His267A proton donor
Lys266A proton acceptor, proton donor, proton relay
His592B proton acceptor, proton donor
His267A proton acceptor

Chemical Components

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

Step 1. Solvent deprotoantes His592 which triggers the subsequent deprotonation of His267 and the substrate amine group. The amine then attacks the aldehyde group of 10-f-THF.

Step 2. The tetrahedral intermediate collapses to form the product and the cofactor is protonated by Lys266. The native state of the enzyme is regenerated.

Products.

Contributors

Peter Sarkies, Craig Porter, Gemma L. Holliday, Amelia Brasnett