Function and Biology

TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site

Source organism: Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Biochemical function: aspartic-type endopeptidase activity
Biological process: proteolysis
Cellular component: not assigned

EC 2.7.7.49: RNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Comments:
  • Catalyzes RNA-template-directed extension of the 3'-end of a DNA strand by one deoxynucleotide at a time.
  • Cannot initiate a chain de novo.
  • Requires a RNA or DNA primer.
  • DNA can also serve as template.
  • See also EC 2.7.7.7.
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • DNA nucleotidyltransferase (RNA-directed)
  • RNA revertase
  • RNA-dependent DNA polymerase
  • RNA-dependent deoxyribonucleate nucleotidyltransferase
  • RNA-instructed DNA polymerase
  • RT
  • Reverse transcriptase
  • Revertase

EC 3.1.13.2: Exoribonuclease H

Reaction catalysed:
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
Comments:
  • This is a secondary reaction to the RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end performed by EC 3.1.26.13.
Systematic name:
-

EC 3.4.23.16: HIV-1 retropepsin

Reaction catalysed:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Comments:
  • Present in human immunodeficiency virus type 1.
  • Contributes to the maturation of the viral particle, and is a target of antiviral drugs.
  • Active enzyme is a dimer of identical 11-kDa subunits.
  • Similar enzymes occur in other retroviruses.
  • Belongs to peptidase family A2.
Alternative Name(s):
  • HIV aspartyl protease
  • HIV proteinase
  • HIV-1 protease
  • HIV-2 protease
  • Gag protease
  • Human immunodeficiency virus type 1 protease
  • Retroproteinase

EC 2.7.7.7: DNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Comments:
  • Catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • Cannot initiate a chain de novo.
  • Requires a primer which may be DNA or RNA.
  • See also EC 2.7.7.49.
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • DNA duplicase
  • DNA nucleotidyltransferase
  • DNA nucleotidyltransferase (DNA-directed)
  • DNA polymerase
  • DNA polymerase alpha
  • DNA polymerase beta
  • DNA polymerase gamma
  • DNA polymerase I
  • DNA polymerase II
  • DNA polymerase III
  • DNA replicase
  • DNA-dependent DNA polymerase
  • Klenow fragment
  • Taq DNA polymerase
  • Taq Pol I
  • Tca DNA polymerase
  • Deoxynucleate polymerase
  • Deoxyribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid duplicase
  • Deoxyribonucleic acid polymerase
  • Deoxyribonucleic duplicase
  • Deoxyribonucleic polymerase
  • Deoxyribonucleic polymerase I
  • Duplicase
  • Sequenase

EC 3.1.26.13: Retroviral ribonuclease H

Reaction catalysed:
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Comments:
  • Retroviral reverse transcriptase is a multifunctional enzyme responsible for viral replication.
  • To perform this task the enzyme combines two distinct activities.
  • The polymerase domain (EC 2.7.7.49) occupies the N-terminal two- thirds of the reverse transcriptase whereas the ribonuclease H domain comprises the C-terminal remaining one-third.
  • The RNase H domain of Moloney murine leukemia virus and Human immunodeficiency virus display two metal binding sites.
Systematic name:
-
Alternative Name(s):
  • RT/RNase H
  • Retroviral reverse transcriptase RNaseH
  • HIV RNase H

GO terms

Biochemical function:
Biological process:
Cellular component:
  • not assigned

Sequence family

Pfam Protein family (Pfam)
PF00077
Domain description: Retroviral aspartyl protease
Occurring in:
  1. Protease
1 copy of Pfam domain PF00077 (Retroviral aspartyl protease) in Protease in PDB 4k4q.

InterPro InterPro annotations
IPR021109
Domain description: Aspartic peptidase domain superfamily
Occurring in:
  1. Protease
IPR001969
Domain description: Aspartic peptidase, active site
Occurring in:
  1. Protease
IPR001995
Domain description: Peptidase A2A, retrovirus, catalytic
Occurring in:
  1. Protease
IPR018061
Domain description: Retropepsins
Occurring in:
  1. Protease
IPR034170
Domain description: Retropepsin-like catalytic domain
Occurring in:
  1. Protease

Structure domain

CATH CATH domain
2.40.70.10
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Cathepsin D, subunit A; domain 1
Homology: Acid Proteases
Occurring in:
  1. Protease
1 copy of CATH domain 2.40.70.10 (Cathepsin D, subunit A; domain 1) in Protease in PDB 4k4q.