Other Proteins Compared with Avian Sarcoma Virus Integrase
ASV and HIV IN belong to a superfamily of other DNA- and RNA-binding proteins, such as MuA
transposase, RuvC resolvase, the Klenow fragment of DNA polymerase I, and the ribonuclease-H
(RNase H) domain of HIV-1 reverse transcriptase (RT). All of these proteins cut or cut-and-splice
DNA or RNA, the nucleic acids which store or transfer genetic information in all living organisms.
Some of these proteins, such as IN and RT, are only used extensively by viruses, whereas others are
extensively used in organisms as diverse as bacteria and human beings. Comparisons between enzymes used
in life forms as unrelated to us as viruses help us not only to learn how to combat viruses with novel drugs,
but also to understand how our own enzymes function as well.
A structural comparison of IN and MuA transposase.
MuA transposase is considerably larger than the catalytic core domain of IN, but when longer loops are
"trimmed" (as shown in the image), a high degree of similarity is seen. This suggests that these enzymes
work in a similar manner. The backbone of the proteins are shown as ribbons; the
active site residues are shown as stick figures. We believe that, unlike
our structures of ASV IN, these structures show inactive conformations of the proteins.
This is a close-up view of the aligned active sites of ASV and HIV-1 INs. ASV IN is shown in light blue and
dark blue as the "apoenzyme" (no required metal bound) and the activated enzyme with magnesium (Mg2+)
in green, or with manganese (Mn2+) in purple. These metals are
essential cations, called cofactors, without which IN is inactive. HIV-1 IN, shown in red, is aligned
compared with the ASV IN backbone, but the active site side chains are significantly out of alignment. It is
unlikely that HIV-1 IN can bind the required cofactors while in this conformation.
This is a close-up view of the active sites of ASV IN, the Klenow fragment of DNA polymerase I, and the RNase H
domain of HIV-1 RT. These enzymes process nucleic acids (RNA or DNA) with the help of bound metal cations,
shown as colored spheres. (The smaller sphere in red depicts a water molecule that we consistently see bound
(coordinated) with the zinc that binds to IN.) Although these proteins differ quite a bit in overall size and in
the identity of the specific side chains that bind metal cations, all active sites superimpose
remarkably well.
This is another view of the active sites of ASV IN (green) and the Klenow fragment
of DNA polymerase I (purple), both with two zinc cations bound. The Klenow fragment has a single DNA nucleotide
(thymidine, "THY") in its active site. The small red sphere in the center shows a water molecule held between
the zinc cations in the ASV IN structure. Although no DNA substrate has been crystallized with any IN, we think
this remarkable structural superposition is no coincidence. This zinc-coordinated water molecule might be replaced
by substrate when IN is processing DNA. *The Klenow fragment coordinates with zinc (above) and with thymidine (here)
are shown courtesy of Dr. L. Beese (Dr. T. Steitz's laboratory). Images and comparisons of ASV IN with this
structure are original work of the MSL.
Back to the ASV IN home page.
If you have questions or comments about the Integrase Project web site,
contact: Jerry N. Alexandratos at alexandr@ncifcrf.gov.