HIV-1 retropepsin

 

HIV-1 protease is an essential part of the viral replication machinery, responsible for processing translated proteins into functional enzymes. It is part of the apartyl protease family. It cleaves the amide bond of proteins between non-specific pairs of residues.

 

Reference Protein and Structure

Sequence
P04585 UniProt (2.7.7.-, 2.7.7.7, 2.7.7.49, 3.1.-.-, 3.1.13.2, 3.1.26.13, 3.4.23.16) IPR021109 (Sequence Homologues) (PDB Homologues)
Biological species
HIV-1 M:B_HXB2R (Virus) Uniprot
PDB
1a30 - HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR (2.0 Å) PDBe PDBsum 1a30
Catalytic CATH Domains
2.40.70.10 CATHdb (see all for 1a30)
Click To Show Structure

Enzyme Reaction (EC:3.4.23.16)

water
CHEBI:15377ChEBI
+
dipeptide zwitterion
CHEBI:90799ChEBI
→
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
+
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
Alternative enzyme names: HIV aspartyl protease, HIV proteinase, HIV-1 protease, HIV-2 protease, Gag protease, Human immunodeficiency virus type 1 protease, Retroproteinase,

Enzyme Mechanism

Introduction

Equivalent aspartate residues from each chain are involved in catalysis. In the first step, one acts as a base to deprotonate the nucleophilic water molecule, while the other acts as an acid to protonate the carbonyl group and activate it. In the second step, the acid/base roles are reversed. The carbonyl group is reformed and the C-N bond of the substrate is broken.

Both aspartate residues are required for catalytic activity. One must be protonated and the other deprotonated. Dissociation of the active dimeric form results in a complete loss of activity. Note that since this is a homodimer the assignment of chains A and B is arbitrary.

Thr26/Thr26' and Gly27/Gly27' have previously been implicated in the catalytic mechanism. However, they are more likely to be involved in stabilising the active site (Thr26/Thr26') and positioning the substrate (Gly27/Gly27').

Catalytic Residues Roles

UniProt PDB* (1a30)
Asp513 Asp25A Deprotonates the nucleophilic water molecule in the first step; protonates the leaving group in the second step. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Thr514, Thr514 Thr26A, Thr26B Helps stabilise the negatively charged transition state. electrostatic stabiliser, transition state stabiliser
Gly515 (main-N), Gly515 (main-N) Gly27B (main-N), Gly27A (main-N) Stabilise and hold the catalytic aspartates in position. hydrogen bond donor, electrostatic stabiliser
Asp513 Asp25B Protonates the carbonyl in the first step; deprotonates the resulting alcohol in the second step. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
*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, bimolecular elimination, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Liu H et al. (1996), J Mol Biol, 261, 454-469. A Combined Quantum/Classical Molecular Dynamics Study of the Catalytic Mechanism of HIV Protease. DOI:10.1006/jmbi.1996.0476. PMID:8780786.
  2. Krzemińska A et al. (2016), J Am Chem Soc, 138, 16283-16298. Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease. DOI:10.1021/jacs.6b06856. PMID:27935692.
  3. Tie Y et al. (2004), J Mol Biol, 338, 341-352. High Resolution Crystal Structures of HIV-1 Protease with a Potent Non-peptide Inhibitor (UIC-94017) Active Against Multi-drug-resistant Clinical Strains. DOI:10.1016/j.jmb.2004.02.052. PMID:15066436.
  4. Piana S et al. (2002), J Mol Biol, 319, 567-583. Role of Conformational Fluctuations in the Enzymatic Reaction of HIV-1 Protease. DOI:10.1016/s0022-2836(02)00301-7. PMID:12051929.
  5. Mager PP (2001), Med Res Rev, 21, 348-353. The active site of HIV-1 protease. DOI:10.1002/med.1012. PMID:11410934.
  6. Silva AM et al. (1996), J Mol Biol, 255, 321-340. Inhibition and catalytic mechanism of HIV-1 aspartic protease. DOI:10.1006/jmbi.1996.0026. PMID:8551523.
  7. Blundell TL et al. (1990), Trends Biochem Sci, 15, 425-430. The 3-D structure of HIV-1 proteinase and the design of antiviral agents for the treatment of AIDS. DOI:10.1016/0968-0004(90)90280-o. PMID:2278102.

Step 1. Asp25A deprotonates water, which then attacks the carbonyl carbon of the peptide bond in a nucleophilic addition, the resulting oxyanion then deprotonates Asp25B.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp25A hydrogen bond acceptor
Gly27A (main-N) hydrogen bond donor
Asp25B hydrogen bond acceptor, hydrogen bond donor
Gly27B (main-N) hydrogen bond donor, electrostatic stabiliser
Thr26A transition state stabiliser
Thr26B transition state stabiliser
Asp25B proton donor
Asp25A proton acceptor

Chemical Components

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

Step 2. Asp25B deprotonates the alcohol group of the intermediate, initiating an elimination that cleaves the peptide bond. The N-terminal product then deprotonates Asp25A.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr26A electrostatic stabiliser
Thr26B electrostatic stabiliser
Asp25A hydrogen bond donor, hydrogen bond acceptor
Gly27A (main-N) hydrogen bond donor, electrostatic stabiliser
Asp25B hydrogen bond acceptor
Gly27B (main-N) hydrogen bond donor
Asp25A proton donor
Asp25B proton acceptor

Chemical Components

proton transfer, ingold: bimolecular elimination, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Asp25A deprotonates water, which then attacks the carbonyl carbon of the peptide bond in a nucleophilic addition, the resulting oxyanion then deprotonates Asp25B.

Step 2. Asp25B deprotonates the alcohol group of the intermediate, initiating an elimination that cleaves the peptide bond. The N-terminal product then deprotonates Asp25A.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, James W. Murray, Anna Waters, Craig Porter, Charity Hornby