Membrane dipeptidase

 

Renal Dipeptidase (hrDP), sourced from Homo sapiens, is a membrane-bound glyco-protein involved in hydrolysis of dipeptides. Hydrophobic dipeptides are cleaved preferentially, including prolyl amino acids. In the renal cortex, it is bound to the microvillar membranes in the brush-border region of proximal tubules. hrDP is involved in the hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. It also plays important roles in the renal metabolism of glutathione.

 

Reference Protein and Structure

Sequence
P16444 UniProt (3.4.13.19, 3.5.2.6) IPR028536 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1itq - HUMAN RENAL DIPEPTIDASE (2.3 Å) PDBe PDBsum 1itq
Catalytic CATH Domains
3.20.20.140 CATHdb (see all for 1itq)
Cofactors
Zinc(2+) (2) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:3.4.13.19)

L-aminoacyl-L-amino acid zwitterion
CHEBI:77460ChEBI
+
water
CHEBI:15377ChEBI
→
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
Alternative enzyme names: MDP, Aminodipeptidase, Dehydropeptidase I (DPH I), Dipeptidase, Dipeptide hydrolase, Dipeptidyl hydrolase, Glycosyl-phosphatidylinositol-anchored renal dipeptidase, Nonspecific dipeptidase, Renal dipeptidase, Microsomal dipeptidase, Dehydropeptidase I, DPH I,

Enzyme Mechanism

Introduction

Asp 288 deprotonates a water molecule in the active site. The activated water molecule performs nucleophilic attack upon the carbonyl group of the amide. An oxyanion tetrahedral transition state is formed. This is stabilised electrostatically by protonated His 152. The tetrahedral transition state then collapses and the amine group of the scissile amide bond leaves.

Catalytic Residues Roles

UniProt PDB* (1itq)
Glu141 Glu125A Acts as a bridging ligand between the two zinc ions. metal ligand
His168 His152A Protonated His 152 electrostatically stabilises the oxyanion tetrahedral transition state. hydrogen bond donor, electrostatic stabiliser
His214, His235 His198A, His219A Forms part of the zinc 2 binding site. metal ligand
Asp304 Asp288A Asp 288 activates a water molecule in the active site by deprotonation. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Asp38, His36 Asp22A, His20A Forms part of the zinc 1 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, overall reactant used, intermediate formation, bimolecular nucleophilic addition, unimolecular elimination by the conjugate base, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Nitanai Y et al. (2002), J Mol Biol, 321, 177-184. Crystal Structure of Human Renal Dipeptidase Involved in β-Lactam Hydrolysis. DOI:10.1016/s0022-2836(02)00632-0. PMID:12144777.
  2. Liao RZ et al. (2010), J Inorg Biochem, 104, 37-46. Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: mechanistic insights from DFT calculations. DOI:10.1016/j.jinorgbio.2009.09.025. PMID:19879002.

Step 1. Asp288 deprotonates the zinc activated water molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp22A metal ligand
Glu125A metal ligand
His20A metal ligand
His198A metal ligand
His219A metal ligand
His152A hydrogen bond donor
Asp288A hydrogen bond acceptor
Asp288A proton acceptor

Chemical Components

proton transfer, overall reactant used, intermediate formation

Step 2. The activated hydroxide attacks the peptide carbonyl in a nucleophilic addition.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp22A metal ligand
Glu125A metal ligand
His20A metal ligand
His198A metal ligand
His219A metal ligand
His152A hydrogen bond donor, electrostatic stabiliser
Asp288A hydrogen bond donor

Chemical Components

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

Step 3. The oxyanion initiates an elimination that cleaves the peptide bond, releasing the amino acid products, the N-terminus then protonates from Asp288

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp22A metal ligand
Glu125A metal ligand
His20A metal ligand
His198A metal ligand
His219A metal ligand
His152A hydrogen bond donor, electrostatic stabiliser
Asp288A hydrogen bond donor, proton donor

Chemical Components

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

Step 1. Asp288 deprotonates the zinc activated water molecule.

Step 2. The activated hydroxide attacks the peptide carbonyl in a nucleophilic addition.

Step 3. The oxyanion initiates an elimination that cleaves the peptide bond, releasing the amino acid products, the N-terminus then protonates from Asp288

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Fiona J. E. Morgan, James Torrance, Charity Hornby