PDBe 3qin

X-ray diffraction
1.7Å resolution

Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor


Function and Biology Details

Reactions 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. 
Endonucleolytic cleavage to 5'-phosphomonoester. 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). 
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
p15; Ribonuclease HI Chain: A
Molecule details ›
Chain: A
Length: 150 amino acids
Theoretical weight: 16.92 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
  • Canonical: P04585 (Residues: 1014-1093, 1105-1148; Coverage: 9%)
  • Canonical: P0A7Y4 (Residues: 79-103; Coverage: 16%)
  • nullnull
Gene names: JW0204, b0214, dasF, gag-pol, herA, rnh, rnhA, sdrA
Structure domains: Nucleotidyltransferase; domain 5

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: I212121
Unit cell:
a: 38.841Å b: 90.37Å c: 111.922Å
α: 90° β: 90° γ: 90°
R R work R free
0.223 0.22 0.253
Expression system: Escherichia coli BL21(DE3)