2QKB: Human Rnase H Catalytic Domain Mutant D210n In Complex With 20-Mer RnaDNA HYBRID

We report here crystal structures of human RNase H1 complexed with an RNA/DNA substrate. Unlike B. halodurans RNase H1, human RNase H1 has a basic protrusion, which forms a DNA-binding channel and together with the conserved phosphate-binding pocket confers specificity for the B form and 2'-deoxy DNA. The RNA strand is recognized by four consecutive 2'-OH groups and cleaved by a two-metal ion mechanism. Although RNase H1 is overall positively charged, the substrate interface is neutral to acidic in character, which likely contributes to the catalytic specificity. Positions of the scissile phosphate and two catalytic metal ions are interdependent and highly coupled. Modeling of HIV reverse transcriptase (RT) with RNA/DNA in its RNase H active site suggests that the substrate cannot simultaneously occupy the polymerase active site and must undergo a conformational change to toggle between the two catalytic centers. The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors.
PDB ID: 2QKBDownload
MMDB ID: 60557
PDB Deposition Date: 2007/7/10
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2QKB: tetrameric; determined by author and by software (PISA)
Molecular Components in 2QKB
Label Count Molecule
Proteins (2 molecules)
Ribonuclease H1(Gene symbol: RNASEH1)
Molecule annotation
Nucleotides(2 molecules)
5'- R(*gp*gp*ap*gp*up*gp*cp*gp*ap*cp*ap*cp*cp*up*gp*ap*up*up*cp *c)-3')
Molecule annotation
5'- D(*dgp*dgp*dap*dap*dtp*dcp*dap*dgp*dgp*dtp*dgp*dtp*dcp*dgp* Dcp*dap*dcp*dtp*dcp*dt)-3'
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB