Adenylate cyclase

 

Adenylate cyclase converts adenosine triphosphate (ATP) into cyclic adenosine monophosphate (cAMP), a ubiquitous second messenger that regulates many functions. Many signalling pathways triggered by hormones and other biological processes converge on and regulate the integral membrane enzyme, including those of the heterotrimeric GTP-binding proteins. There are over 30 related proteins, including bacterial and fungal adenylyl cyclases as well as guanylyl cyclases.

 

Reference Protein and Structure

Sequences
P26769 UniProt (4.6.1.1)
P30803 UniProt (4.6.1.1) IPR030672 (Sequence Homologues) (PDB Homologues)
Biological species
Rattus norvegicus (Norway rat) Uniprot
PDB
1cju - COMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENYLYL CYCLASE: COMPLEX WITH BETA-L-2',3'-DIDEOXYATP AND MG (2.8 Å) PDBe PDBsum 1cju
Catalytic CATH Domains
3.30.70.1230 CATHdb (see all for 1cju)
Cofactors
Magnesium(2+) (2) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:4.6.1.1)

ATP(4-)
CHEBI:30616ChEBI
→
diphosphate(3-)
CHEBI:33019ChEBI
+
3',5'-cyclic AMP(1-)
CHEBI:58165ChEBI
Alternative enzyme names: 3',5'-cyclic AMP synthetase, Adenyl cyclase, Adenylylcyclase, ATP pyrophosphate-lyase, Adenylyl cyclase, ATP diphosphate-lyase (cyclizing),

Enzyme Mechanism

Introduction

The alpha-phosphate deprotonates the 3'-hydroxyl of ATP, which in turn attacks the phosphorus atom in a nucleophilic addition, forming a cyclic pentacoordinate phosphorus intermediate. The cyclic pentacoordinate phosphorus intermediate collapses eliminating the diphosphate molecule. One or two magnesium ions have been suggested as playing a part in the catalytic mechanism, for example by stabilising the transition state, but they are not present in the PDB file.

Catalytic Residues Roles

UniProt PDB* (1cju)
Asp521 Asp440(77)A Forms part of the Magnesium 1 binding site. metal ligand
Arg1029 Arg1029(160)B Stabilises negatively charged transition state. Ensures that the transition state for the concerted phosphoryl transfer is "tight". electrostatic stabiliser
Asp477, Asp521, Lys1065 Asp396(33)A, Asp440(77)A, Lys1065(196)B Facilitate proton transfer from the ribosyl 3′O to the γ phosphate O2-gamma by decreasing the difference in the pKa values of the proton donor and acceptor and by anchoring the metal ions and hence reducing the free energy barrier for the proton transfer. metal ligand, proton acceptor, proton donor
Ile478 (main-C) Ile397(34)A (main-C) Forms part of the Magnesium 2 binding site. metal ligand
*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

cyclisation, proton transfer, intramolecular elimination

References

  1. Tesmer JJ et al. (1997), Science, 278, 1907-1916. Crystal Structure of the Catalytic Domains of Adenylyl Cyclase in a Complex with Gs·GTPS. DOI:10.1126/science.278.5345.1907. PMID:9417641.
  2. Hahn DK et al. (2015), Biochemistry, 54, 6252-6262. Catalytic Mechanism of Mammalian Adenylyl Cyclase: A Computational Investigation. DOI:10.1021/acs.biochem.5b00655. PMID:26393535.
  3. Lee Y et al. (2004), J Phys Chem B, 108, 4508-4515. Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase. DOI:10.1021/jp036564h.
  4. Serfass L et al. (2001), Arch Biochem Biophys, 387, 47-56. Calcium Ion Downregulates Soluble Guanylyl Cyclase Activity: Evidence for a Two-metal Ion Catalytic Mechanism. DOI:10.1006/abbi.2000.2090. PMID:11368183.
  5. Tesmer JJ et al. (2000), Biochemistry, 39, 14464-14471. Molecular basis for P-site inhibition of adenylyl cyclase. PMID:11087399.
  6. Tesmer JJ et al. (1999), Science, 285, 756-760. Two-Metal-Ion Catalysis in Adenylyl Cyclase. DOI:10.1126/science.285.5428.756. PMID:10427002.
  7. Hurley JH (1999), J Biol Chem, 274, 7599-7602. Structure, Mechanism, and Regulation of Mammalian Adenylyl Cyclase. DOI:10.1074/jbc.274.12.7599.
  8. Yan SZ et al. (1997), J Biol Chem, 272, 12342-12349. The Conserved Asparagine and Arginine Are Essential for Catalysis of Mammalian Adenylyl Cyclase. DOI:10.1074/jbc.272.19.12342. PMID:9139678.

Step 1. Asp396 deprotonates the 3'-hydroxyl of ATP, which in turn attacks the phosphorus atom in a nucleophilic addition, forming a cyclic pentacoordinate phosphorus intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp440(77)A metal ligand
Asp396(33)A metal ligand
Ile397(34)A (main-C) metal ligand
Arg1029(160)B electrostatic stabiliser
Lys1065(196)B electrostatic stabiliser
Asp396(33)A proton acceptor

Chemical Components

cyclisation, proton transfer, ingold: intramolecular elimination

Step 2. Inferred return step to regenerate the active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp440(77)A metal ligand
Asp396(33)A metal ligand
Ile397(34)A (main-C) metal ligand
Asp396(33)A proton donor

Chemical Components

proton transfer
Download: Image, Marvin File

Step 1. Asp396 deprotonates the 3'-hydroxyl of ATP, which in turn attacks the phosphorus atom in a nucleophilic addition, forming a cyclic pentacoordinate phosphorus intermediate.

Step 2. Inferred return step to regenerate the active site.

Products.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, James W. Murray, Craig Porter