Aspartate carbamoyltransferase

 

Aspartate carbamoyltransferase catalyses the formation of N-carbamoyl-L-aspartate and inorganic phosphate from carbamoyl phosphate and L-aspartate. In many prokaryotes such as E. coli this reaction is the committed step in pyrimidine biosynthesis.

The E. coli protein exits as a heterododecamer (2C3:3R2) of six catalytic PyrB chains organized as two trimers (C3), and six regulatory PyrI chains organized as three dimers (R2). The PyrI chain is involved in the allosteric regulation of the catalytic reaction and binds one zinc ion. E. coli aspartate transcarbamoylase is feedback inhibited by CTP and by UTP in the presence of CTP.

 

Reference Protein and Structure

Sequences
P0A786 UniProt (2.1.3.2)
P0A7F3 UniProt IPR002082 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1at1 - CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL P*H (2.8 Å) PDBe PDBsum 1at1
Catalytic CATH Domains
3.40.50.1370 CATHdb (see all for 1at1)
Click To Show Structure

Enzyme Reaction (EC:2.1.3.2)

L-aspartate(1-)
CHEBI:29991ChEBI
+
carbamoyl phosphate(2-)
CHEBI:58228ChEBI
→
N-carbamoyl-L-aspartate(2-)
CHEBI:32814ChEBI
+
hydron
CHEBI:15378ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
Alternative enzyme names: L-aspartate transcarbamoylase, L-aspartate transcarbamylase, ATCase, Aspartate carbamyltransferase, Aspartate transcarbamoylase, Aspartate transcarbamylase, Aspartic acid transcarbamoylase, Aspartic carbamyltransferase, Aspartic transcarbamylase, Carbamoylaspartotranskinase, Carbamylaspartotranskinase,

Enzyme Mechanism

Introduction

Lysine deprotonates the amino group of aspartate to activate it as a nucleophile. Three other residues interact with the carbonyl oxygen of the carbamoyl phosphate, enhancing the electrophilicity of the carbonyl carbon for attack by aspartate. An arginine residue stabilises the developing negative charge of the oxygen as the phosphate leaving group is expelled.

Catalytic Residues Roles

UniProt PDB* (1at1)
Arg55 Arg54A Stabilises the developing negative charge of the oxygen as the phosphate leaving group is expelled. electrostatic stabiliser
Thr56, His135, Arg106 Thr55A, His134A, Arg105A Enhances electrophilicity of carbonyl carbon. increase electrophilicity, electrostatic stabiliser
Lys85 Lys84A(AA) Deprotonates the amino group of aspartate. proton shuttle (general acid/base)
*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. Lipscomb WN et al. (2012), Acc Chem Res, 45, 444-453. Structure and Mechanisms of Escherichia coli Aspartate Transcarbamoylase. DOI:10.1021/ar200166p. PMID:22011033.
  2. Kantrowitz ER (2012), Arch Biochem Biophys, 519, 81-90. Allostery and cooperativity in Escherichia coli aspartate transcarbamoylase. DOI:10.1016/j.abb.2011.10.024. PMID:22198283.
  3. Peterson AW et al. (2012), Biochemistry, 51, 4776-4778. A Second Allosteric Site inEscherichia coliAspartate Transcarbamoylase. DOI:10.1021/bi3006219. PMID:22667327.
  4. West JM et al. (2008), J Mol Biol, 384, 206-218. Time Evolution of the Quaternary Structure of Escherichia coli Aspartate Transcarbamoylase upon Reaction with the Natural Substrates and a Slow, Tight-Binding Inhibitor. DOI:10.1016/j.jmb.2008.09.022. PMID:18823998.
  5. Macol CP et al. (2001), Nat Struct Biol, 8, 423-426. Direct structural evidence for a concerted allosteric transition in Escherichia coli aspartate transcarbamoylase. DOI:10.1038/87582. PMID:11323717.
  6. Jin L et al. (1999), Proteins, 37, 729-742. Insights into the mechanisms of catalysis and heterotropic regulation ofEscherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogueN-phosphonacetyl-L-aspartate at 2.1 ? DOI:10.1002/(sici)1097-0134(19991201)37:4<729::aid-prot21>3.0.co;2-f. PMID:10651286.
  7. Stebbins JW et al. (1989), Biochemistry, 28, 2592-2600. Three residues involved in binding and catalysis in the carbamyl phosphate binding site of Escherichia coli aspartate transcarbamylase. PMID:2659074.

Step 1.

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Catalytic Residues Roles

Residue Roles
Lys84A(AA) proton shuttle (general acid/base)
Arg54A electrostatic stabiliser
Thr55A electrostatic stabiliser
Arg105A electrostatic stabiliser
His134A electrostatic stabiliser
Thr55A increase electrophilicity
Arg105A increase electrophilicity
His134A increase electrophilicity

Chemical Components

Step 1.

Contributors

Stuart Lucas, Gemma L. Holliday