Retroviral integrase (IN) is an
enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...
produced by a
retrovirus (such as
HIV
The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immu ...
) that
integrates—forms
covalent links between—its genetic information into that of the host
cell it infects. Retroviral INs are not to be confused with
phage integrases (
recombinases)
used in biotechnology, such as
λ phage
''Enterobacteria phage λ'' (lambda phage, coliphage λ, officially ''Escherichia virus Lambda'') is a bacterial virus, or bacteriophage, that infects the bacterial species '' Escherichia coli'' (''E. coli''). It was discovered by Esther Lede ...
integrase, as discussed in
site-specific recombination.
The
macromolecular complex of an IN
macromolecule bound to the ends of the viral DNA ends has been referred to as the ''
intasome''; IN is a key component in this and the retroviral
pre-integration complex.
Structure
All retroviral IN proteins contain three canonical domains, connected by flexible linkers:
● an
N-terminal HH-CC zinc-binding domain (a three-helical bundle stabilized by coordination of a Zn(II) cation)
● a catalytic core domain (RNaseH fold)
● a
C-terminal
The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...
DNA-binding domain (
SH3 fold).
Crystal and NMR structures of the individual domains and 2-domain constructs of integrases from HIV-1, HIV-2,
SIV, and
Rous Sarcoma Virus (RSV) have been reported, with the first structures determined in 1994.
Biochemical data and structural data suggest that retroviral IN functions as a
tetramer (dimer-of-dimers), with all three domains being important for multimerization and viral DNA binding. In addition, several host cellular proteins have been shown to interact with IN to facilitate the integration process: e.g., the host factor, human chromatin-associated protein
LEDGF, tightly binds HIV IN and directs the HIV pre-integration complex towards highly expressed genes for integration.
Human foamy virus (HFV), an agent harmless to humans, has an integrase similar to HIV IN and is therefore a model of HIV IN function; a 2010 crystal structure of the HFV integrase assembled on viral DNA ends has been determined.
Function and mechanism
Integration occurs following production of the double-stranded linear viral DNA by the viral RNA/DNA-dependent DNA polymerase
reverse transcriptase.
The main function of IN is to insert the viral DNA into the host chromosomal DNA, an essential step for
HIV
The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immu ...
replication. Integration is a "point of no return" for the cell, which becomes a permanent carrier of the viral genome (provirus). Integration is in part responsible for the persistence of retroviral infections.
After integration, the viral gene expression and particle production may take place immediately or at some point in the future, the timing depends on the activity of the chromosomal locus hosting the provirus.
Retroviral INs catalyzes two reactions:
● 3'-processing, in which two or three nucleotides are removed from one or both 3' ends of the viral DNA to expose an invariant CA dinucleotide at both 3'-ends of the viral DNA.
● the strand transfer reaction, in which the processed 3' ends of the viral DNA are covalently ligated to host chromosomal DNA.
Both reactions are catalyzed in the same active site, and involve
transesterification without involving a
covalent protein-DNA intermediate (in contrast to
Ser/Tyr recombinase-catalyzed reactions.
In HIV
]
HIV
The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immu ...
integrase is a 32kDa viral protein consisting of three domains-
N-terminus, catalytic core domain, and C-terminus, which each have distinct properties and functions contributing to the efficacy of HIV integrase.
The N-terminus is composed of 50 amino acid residues which contain a conserved histidine, histidine, cytosine, cytosine sequence which chelates zinc ions, furthermore enhancing the enzymatic activity of the catalytic core domain.
As metal chelation is vital in integrase efficacy, it is a target for the development of retroviral therapies.
The catalytic core domain, like the N-terminus, contains highly conserved amino acid residues -Asp64, Asp116, Glu152- as the conserved DDE (Asp-Asp-Glu) motif contributes to the endonuclease and polynucleotide transferase functions of integrase. Mutations in these regions inactivates integrase and prevents genome integration.
The C-terminus domain binds to host DNA non-specifically and stabilizes the integration complex.
Integration mechanism
Following synthesis of HIV's doubled stranded DNA genome, integrase binds to the long tandem repeats flanking the genome on both ends. Using its endonucleolytic activity, integrase cleaves a di or trinucleotide from both 3' ends of the genome in a processing known as 3'-processing.
The specificity of cleavage is improved through the use of cofactors such as Mn
2+ and Mg
2+ which interact with the DDE motif of the catalytic core domain, acting as cofactors to integrase function.
The newly generated 3'OH groups disrupt the host DNA's phosphodiester linkages through SN2-type nucleophilic attack.
The 3' ends are covalently linked to the target DNA. The 5' over hangs of the viral genome are then cleaved using host repair enzymes, those same enzymes are believed to be responsible for the integration of the 5' end into the host genome forming the provirus.
Antiretroviral therapy
In November 2005, data from a
phase 2 study of an investigational HIV
integrase inhibitor,
MK-0518, demonstrated that the compound has potent antiviral activity. On October 12, 2007, the Food and Drug Administration (U.S.) approved the integrase inhibitor
Raltegravir (MK-0518, brand name Isentress). The second integrase inhibitor,
elvitegravir, was approved in the U.S. in August 2012.
See also
*
Integrase inhibitor
*
Integron
References
Further reading
*
External links
* PDB-101 Molecule of the Month
135 HIV Integrase*
{{Viral proteins
Virology
Enzymes
Viral enzymes