Peptidyl-dipeptidase A

 

Angiotensin I-converting enzymes (ACEs) are zinc metalloproteases that cleave dipeptides from the C-termini of short peptide hormones. In humans, ACE has an important role in regulating blood pressure and heart maintenance by catalysing the production of the hypertensive peptide angiotensin II from angiotensin I and the destruction of the hypotensive peptide bradykinin. ACE has minimal sequence homology with other zinc proteases, but it does share the HExxH zinc-binding motif of the well-studied zinc metalloprotease thermolysin.

 

Reference Protein and Structure

Sequence
P12821 UniProt (3.2.1.-, 3.4.15.1) IPR001548 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1o8a - Crystal Structure of Human Angiotensin Converting Enzyme (Native). (2.0 Å) PDBe PDBsum 1o8a
Catalytic CATH Domains
(see all for 1o8a)
Cofactors
Zinc(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:3.4.15.1)

water
CHEBI:15377ChEBI
+
dipeptide zwitterion
CHEBI:90799ChEBI
→
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
+
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
Alternative enzyme names: ACE, DCP, PDH, Angiotensin I-converting enzyme, Angiotensin converting enzyme, Carboxycathepsin, Dipeptidase, Dipeptide hydrolase, Dipeptidyl carboxypeptidase, Dipeptidyl carboxypeptidase I, Endothelial cell peptidyl dipeptidase, Kininase II, Peptidase P, Peptidyl dipeptidase A, Peptidyl dipeptidase I, Peptidyl dipeptidase-4, Peptidyl dipeptide hydrolase, Peptidyl-dipeptide hydrolase, Peptidyldipeptide hydrolase,

Enzyme Mechanism

Introduction

The catalytic mechanism of ACE has been inferred from that of thermolysin. It is a hydrolytic reaction and proceeds via a general acid-base reaction mechanism. The nucleophilic water molecule is polarised by a Zn(II) ion and is deprotonated by Glu 384 as it attacks the peptide carbonyl. The zinc ion also coordinates the carbonyl and so activates it towards nucleophilic attack. Accumulation of negative charge on the carbonyl oxygen is stabilised by the zinc ion and a hydrogen bond from Tyr 523, His 353, and His 513. A hydrogen bond with the backbone carbonyl of Ala 354 stabilises the positive charge on the amide of the intermediate. The collapse of the tetrahedral intermediate with protonation of the departing amine group by Glu 384 completes the reaction.

Catalytic Residues Roles

UniProt PDB* (1o8a)
Ala959 (main-C) Ala354(318)A (main-C) Stabilizes the positive charge on the amide of the intermediate by hydrogen bonding. hydrogen bond acceptor, electrostatic stabiliser
His958 His353(317)A Stabilises transition state by hydrogen bonding to the carboxylate oxygen atom. hydrogen bond acceptor, electrostatic stabiliser
His1118 His513(477)A Stabilises the intermediate by hydrogen bonding to the carboxylate oxygen atom. hydrogen bond donor, electrostatic stabiliser
Tyr1128 Tyr523(487)A Stabilises the negative charge on the intermediate by hydrogen bonding to the carboxylate oxygen atom. hydrogen bond donor, electrostatic stabiliser
Glu989 Glu384(348)A Activates a water molecule, and donates the proton to the scissile amide nitrogen. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, electrostatic stabiliser
His992, Glu1016, His988 His387(351)A, Glu411(375)A, His383(347)A Forms part of the zinc 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

proton transfer, bimolecular nucleophilic addition, overall reactant used, intermediate formation, unimolecular elimination by the conjugate base, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Tzakos AG et al. (2003), Protein Eng, 16, 993-1003. Structure-function discrimination of the N- and C- catalytic domains of human angiotensin-converting enzyme: implications for Cl- activation and peptide hydrolysis mechanisms. DOI:10.1093/protein/gzg122. PMID:14983080.
  2. Yates CJ et al. (2014), J Biol Chem, 289, 1798-1814. Molecular and Thermodynamic Mechanisms of the Chloride-dependent Human Angiotensin-I-converting Enzyme (ACE). DOI:10.1074/jbc.m113.512335. PMID:24297181.
  3. Masuyer G et al. (2014), FEBS J, 281, 943-956. Crystal structures of highly specific phosphinic tripeptide enantiomers in complex with the angiotensin-I converting enzyme. DOI:10.1111/febs.12660. PMID:24289879.
  4. Brás NF et al. (2014), ACS Catal, 4, 2587-2597. QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme. DOI:10.1021/cs500093h.
  5. Corradi HR et al. (2006), J Mol Biol, 357, 964-974. Crystal Structure of the N Domain of Human Somatic Angiotensin I-converting Enzyme Provides a Structural Basis for Domain-specific Inhibitor Design. DOI:10.1016/j.jmb.2006.01.048. PMID:16476442.
  6. Kim HM et al. (2003), FEBS Lett, 538, 65-70. Crystal structure ofDrosophilaangiotensin I-converting enzyme bound to captopril and lisinopril1. DOI:10.1016/s0014-5793(03)00128-5. PMID:12633854.

Step 1. This enzyme is activated by chloride. Upon chloride binding the salt bridge between Arg522 and Asp465 is broken. This causes the Tyr523 to move, with Arg522, towards the active site. Glu384 deprotonates the zinc activated water molecule. This activated hydroxide then attacks the carbonyl carbon of the peptide bond in a nucleophilic addition.

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Catalytic Residues Roles

Residue Roles
Ala354(318)A (main-C) hydrogen bond acceptor
Glu384(348)A hydrogen bond acceptor
Tyr523(487)A hydrogen bond donor
His513(477)A hydrogen bond donor
His383(347)A metal ligand
His387(351)A metal ligand
Glu411(375)A metal ligand
Glu384(348)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 2. The amine of the peptide bond deprotonates Glu384.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His353(317)A electrostatic stabiliser
Ala354(318)A (main-C) hydrogen bond acceptor, electrostatic stabiliser
Glu384(348)A hydrogen bond donor
Tyr523(487)A hydrogen bond donor, electrostatic stabiliser
His513(477)A hydrogen bond donor, electrostatic stabiliser
His383(347)A metal ligand
His387(351)A metal ligand
Glu411(375)A metal ligand
Glu384(348)A proton donor

Chemical Components

proton transfer, intermediate formation

Step 3. The oxyanion initiates an elimination which cleaves the peptide bond, resulting in both products.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His353(317)A hydrogen bond acceptor, electrostatic stabiliser
Ala354(318)A (main-C) hydrogen bond acceptor, electrostatic stabiliser
Glu384(348)A hydrogen bond acceptor, electrostatic stabiliser
Tyr523(487)A hydrogen bond donor, electrostatic stabiliser
His513(477)A hydrogen bond donor, electrostatic stabiliser
His383(347)A metal ligand
His387(351)A metal ligand
Glu411(375)A metal ligand

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. This enzyme is activated by chloride. Upon chloride binding the salt bridge between Arg522 and Asp465 is broken. This causes the Tyr523 to move, with Arg522, towards the active site. Glu384 deprotonates the zinc activated water molecule. This activated hydroxide then attacks the carbonyl carbon of the peptide bond in a nucleophilic addition.

Step 2. The amine of the peptide bond deprotonates Glu384.

Step 3. The oxyanion initiates an elimination which cleaves the peptide bond, resulting in both products.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Steven Smith, James Torrance, Craig Porter, Yordanos Abeje