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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 substrates, and the enzyme converts the substrates into different molecules known as products ...
produced by a
retrovirus A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptas ...
(such as HIV) that integrates—forms
covalent A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atom ...
links between—its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage integrases (
recombinases Recombinases are genetic recombination enzymes. Site specific recombinases DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes, and to control gene expression. These enzymes, derived from bacteri ...
) used in biotechnology, such as λ phage integrase, as discussed in site-specific recombination. The macromolecular complex of an IN
macromolecule A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The ...
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 The pre-integration complex (PIC) is a nucleoprotein complex of viral genetic material and associated viral and host proteins which is capable of inserting a viral genome into a host genome. The PIC forms after uncoating of a viral particle after e ...
.


Structure

All retroviral IN proteins contain three canonical domains, connected by flexible linkers: ● an
N-terminal The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...
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 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 A tetramer () ('' tetra-'', "four" + '' -mer'', "parts") is an oligomer formed from four monomers or subunits. The associated property is called ''tetramery''. An example from inorganic chemistry is titanium methoxide with the empirical formula ...
(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 A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genom ...
. The main function of IN is to insert the viral DNA into the host chromosomal DNA, an essential step for HIV 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 A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atom ...
protein-DNA intermediate (in contrast to Ser/Tyr recombinase-catalyzed reactions.


In HIV

] HIV integrase is a 32kDa viral protein consisting of three domains-
N-terminus The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...
, 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 Mn2+ and Mg2+ 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 Integrase inhibitors (INIs) are a class of antiretroviral drug designed to block the action of integrase, a viral enzyme that inserts the viral genome into the DNA of the host cell. Since integration is a vital step in retroviral replication, block ...
, 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 Raltegravir, sold under the brand name Isentress, is an antiretroviral medication used, together with other medication, to treat HIV/AIDS. It may also be used, as part of post exposure prophylaxis, to prevent HIV infection following potential ex ...
(MK-0518, brand name Isentress). The second integrase inhibitor, elvitegravir, was approved in the U.S. in August 2012.


See also

*
Integrase inhibitor Integrase inhibitors (INIs) are a class of antiretroviral drug designed to block the action of integrase, a viral enzyme that inserts the viral genome into the DNA of the host cell. Since integration is a vital step in retroviral replication, block ...
* Integron


References


Further reading

*


External links

* PDB-101 Molecule of the Month
135 HIV Integrase
* {{Viral proteins Virology Enzymes Viral enzymes