HIV Integration - Background Information: HIV-1 Integrase

Background Information: HIV-1 Integrase

The integration of HIV DNA into the host DNA is a critical step in the HIV life cycle. Understanding the integration process will provide a framework for gaining insight into multiple potential sites of therapeutic intervention for HIV infection and AIDS. HIV’s enzyme for inserting the DNA version of its genome into the host cell DNA is called its "integrase". HIV-1 integrase catalyzes the “cut-and-paste” action of clipping the host DNA and joining the proviral genome to the clipped ends. This protein, which is 288 amino acids in length, contains three “domains”, in this order:

  1. Amino (N)-terminal domain: Sometimes referred to as a "zinc finger", the N-terminal domain is composed of the conserved HHCC, His, and Cys residues, a motif that serves to bind zinc. The function of the N-terminal domain is not completely clear, but is thought to assist the integrase in forming multimers (fixed agglomerations of multiple integrase molecules).
  1. The central catalytic domain (or "catalytic core"): The catalytic core encompasses the DDE catalytic triad of amino acids, or acid residues, that manage binding with a divalent metal (usually Mg2+ or Mn2-), forming the active catalytic site. In the case of HIV-1 integrase, the residues are Asp64, Asp116, and Glu152. This domain is also well conserved during evolution.

The HIV-1 catalytic domain appears dimeric in solution and in crystal structures. The vast surface area of the dimer interface indicates that it is biologically significant. The insertion sites on each strand of target DNA are separated by 5 base pairs, which parallel to approximately 15 Å for helical B-form DNA, implying that the catalytic domain (or the functional unit) of integrase should contain a pair of active sites separated by a like spacing. This said, the spacing among the active sites in the virtually spherical dimer is, however, apparently not very well-matched with the spacing among the insertion sites on the two strands of target DNA, as examination of crystal structures appears to reveal that the active sites in the dimers are separated by more than 30 Å when measured in a straight line through the proteins, and by an even greater distance when measured around the circumference of the dimer. Under the assumption that the dimer interface is preserved in the functional integrase multimer, at minimum a tetramer of integrase must be required for the complete integration reaction to proceed.

  1. The Carboxy (C)- terminal domain : The C-terminal domain non-specifically binds DNA. Since the sites of integration into the target DNA are relatively non-specific, it is thought that this domain may work together in some fashion with the target DNA. Information retrieved from experiments with chimeric integrases show that recognition of the target site is controlled by the core domain. Cross-linking studies also suggest that the C-terminal domain works together with a subterminal region just inside the very ends of the viral DNA.

During the integration process, the HIV integrase enzyme performs two key catalytic reactions. First is the 3’ processing of the HIV DNA, followed by strand transfer of the HIV DNA into the host DNA. The integration of HIV DNA can occur either in dividing or resting cells, and the HIV integrase enzyme can exist in the form of a monomer, dimer, tetramer, and possibly even higher-order forms (such as octomers). Each HIV particle has an estimated 40 to 100 copies of the integrase enzyme.

Integrase functions are unique to retroviruses; human cells are not required to cut-and-paste pieces of DNA into the genome. For this reason, integrase inhibitors are prime targets for developing drug therapies for HIV infection and AIDS, since inhibition of integrase should not hamper the normal operations in human cells.

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