Editing Integrase

{{Short description|Class of enzymes}}
{{Infobox protein family
| Symbol = Integrase_Zn
| Name = Integrase Zinc binding domain
| image = PDB 1wjd EBI.jpg
| width = 
| caption = solution structure of the N-terminal Zn binding domain of HIV-1 integrase (e form), NMR, 38 structures
| Pfam = PF02022
| Pfam_clan =  
| InterPro = IPR003308
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 1wjb
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
{{Infobox protein family
| Symbol = rve
| Name = Integrase core domain
| image = PDB 1c1a EBI.jpg
| width = 
| caption = Crystal structure of the RSV two-domain integrase.
| Pfam = PF00665
| Pfam_clan = CL0219 
| InterPro = IPR001584
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 2itg
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
{{Infobox protein family
| Symbol = IN_DBD_C
| Name = Integrase DNA binding domain
| image = PDB 1c1a EBI.jpg
| width = 
| caption = Crystal structure of the RSV two-domain integrase.
| Pfam = PF00552
| Pfam_clan =  
| InterPro = IPR001037
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 1ihw
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
'''Retroviral integrase''' ('''IN''') is an [[enzyme]] produced by a [[retrovirus]] (such as [[HIV]]) that [[Retroviral integration|integrates]] (forms [[Covalent bond|covalent]] links between) its genetic information into that of the host [[Cell (biology)|cell]] it infects.<ref>{{cite book | vauthors = Beck BJ, Freudenreich O, Worth JL | chapter = Patients with Human Immunodeficiency Virus Infection and Acquired Immunodeficiency Syndrome |date=2010 | doi = 10.1016/b978-1-4377-1927-7.00026-1 |title = Massachusetts General Hospital Handbook of General Hospital Psychiatry |pages=353–370 |publisher=Elsevier | isbn = 9781437719277 }}</ref> Retroviral INs are not to be confused with [[phage integrase]]s ([[recombinases]]) [[Site-specific recombinase technology|used in biotechnology]], such as [[Lambda phage|λ phage]] integrase, as discussed in [[site-specific recombination]].

The [[Biomolecular complex|macromolecular complex]] of an IN [[macromolecule]] bound to the ends of the viral DNA ends has been referred to as the ''[[wiktionary:intasome#:~:text=Noun,a bacteriophage into a host.|intasome]]''; IN is a key component in this and the retroviral [[pre-integration complex]].<ref>{{cite journal | vauthors = Masuda T | title = Non-Enzymatic Functions of Retroviral Integrase: The Next Target for Novel Anti-HIV Drug Development | journal = Frontiers in Microbiology | volume = 2 | pages = 210 | date = 2011 | pmid = 22016749 | doi = 10.3389/fmicb.2011.00210 | pmc = 3192317 | doi-access = free }}</ref>

== Structure ==
All retroviral IN proteins contain three canonical domains, connected by flexible linkers:<ref name=":0">{{cite journal | vauthors = Jóźwik IK, Passos DO, Lyumkis D | title = Structural Biology of HIV Integrase Strand Transfer Inhibitors | journal = Trends in Pharmacological Sciences | volume = 41 | issue = 9 | pages = 611–626 | date = September 2020 | pmid = 32624197 | doi = 10.1016/j.tips.2020.06.003 | pmc = 7429322 }}</ref><ref name=":1">{{cite journal | vauthors = Delelis O, Carayon K, Saïb A, Deprez E, Mouscadet JF | title = Integrase and integration: biochemical activities of HIV-1 integrase | journal = Retrovirology | volume = 5 | issue = 1 | pages = 114 | date = December 2008 | pmid = 19091057 | pmc = 2615046 | doi = 10.1186/1742-4690-5-114 | doi-access = free }}</ref>

* 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]] DNA-binding domain ([[SH3 domain|SH3 fold]]).

Crystal and NMR structures of the individual domains and 2-domain constructs of integrases from HIV-1, HIV-2, [[Simian immunodeficiency virus|SIV]], and [[Rous Sarcoma Virus]] (RSV) have been reported, with the first structures determined in 1994.<ref>{{cite journal | vauthors = Lodi PJ, Ernst JA, Kuszewski J, Hickman AB, Engelman A, Craigie R, Clore GM, Gronenborn AM | display-authors = 6 | title = Solution structure of the DNA binding domain of HIV-1 integrase | journal = Biochemistry | volume = 34 | issue = 31 | pages = 9826–9833 | date = August 1995 | pmid = 7632683 | doi = 10.1021/bi00031a002 }}</ref><ref name=":2">{{cite journal | vauthors = Choi E, Mallareddy JR, Lu D, Kolluru S | title = Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase | journal = Future Science OA | volume = 4 | issue = 9 | pages = FSO338 | date = October 2018 | pmid = 30416746 | doi = 10.4155/fsoa-2018-0060 | pmc = 6222271 }}</ref> Biochemical data and structural data suggest that retroviral IN functions as a [[Tetrameric protein|tetramer]] (dimer-of-dimers), with all three domains being important for multimerization and viral DNA binding.<ref>{{cite journal | vauthors = Hare S, Di Nunzio F, Labeja A, Wang J, Engelman A, Cherepanov P | title = Structural basis for functional tetramerization of lentiviral integrase | journal = PLOS Pathogens | volume = 5 | issue = 7 | pages = e1000515 | date = July 2009 | pmid = 19609359 | doi = 10.1371/journal.ppat.1000515 | pmc = 2705190 | editor-first = Jeremy | editor-last = Luban | doi-access = free }}</ref> 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 [[PSIP1|LEDGF]], tightly binds HIV IN and directs the HIV pre-integration complex towards highly expressed genes for integration.<ref>{{cite journal | vauthors = Craigie R, Bushman FD | title = HIV DNA integration | journal = Cold Spring Harbor Perspectives in Medicine | volume = 2 | issue = 7 | pages = a006890 | date = July 2012 | pmid = 22762018 | pmc = 3385939 | doi = 10.1101/cshperspect.a006890 }}</ref>

[[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.<ref name=":2" />

== Function and mechanism ==
Integration occurs following production of the double-stranded linear viral DNA by the viral RNA/DNA-dependent DNA polymerase [[reverse transcriptase]].<ref>{{cite journal | vauthors = Burdick RC, Pathak VK | title = Efficient HIV-1 in vitro reverse transcription: optimal capsid stability is required | journal = Signal Transduction and Targeted Therapy | volume = 6 | issue = 1 | pages = 13 | date = January 2021 | pmid = 33436564 | doi = 10.1038/s41392-020-00458-3 | pmc = 7804106 }}</ref>

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.<ref>{{cite journal | vauthors = Maldarelli F | title = The role of HIV integration in viral persistence: no more whistling past the proviral graveyard | journal = The Journal of Clinical Investigation | volume = 126 | issue = 2 | pages = 438–447 | date = February 2016 | pmid = 26829624 | doi = 10.1172/JCI80564 | pmc = 4731194 }}</ref> 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.<ref name=":1" />

Retroviral INs catalyze two reactions:<ref name=":1" />

* 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.
* 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 [[Site specific recombination|Ser/Tyr recombinase-catalyzed reactions]]).<ref name=":1" />

== In HIV ==
[[File:The actual HIV integrase.jpg|thumb|left|alt=HIV catalytic core domain|Structural depiction of the HIV catalytic core domain based on the works of  Feng, L. and Kvaratskhelia, M. from the [https://www.rcsb.org/structure/4DMN protein database]]]

'''[[HIV]]''' '''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.<ref name=":0" />

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.<ref name=":0" /> As metal chelation is vital in integrase efficacy, it is a target for the development of retroviral therapies.<ref name=":0" />

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.<ref name=":0" />

The C-terminus domain binds to host DNA non-specifically and stabilizes the integration complex.<ref name=":0" />

=== 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.<ref name=":3">{{cite journal | vauthors = Mahboubi-Rabbani M, Abbasi M, Hajimahdi Z, Zarghi A | title = HIV-1 Reverse Transcriptase/Integrase Dual Inhibitors: A Review of Recent Advances and Structure-activity Relationship Studies | journal = Iranian Journal of Pharmaceutical Research | volume = 20 | issue = 2 | pages = 333–369 | date = 2021 | pmid = 34567166 | doi = 10.22037/ijpr.2021.115446.15370 | pmc = 8457747 }}</ref> The specificity of cleavage is improved through the use of cofactors such as Mn<sup>2+</sup> and Mg<sup>2+</sup> which interact with the DDE motif of the catalytic core domain, acting as cofactors to integrase function.<ref name=":3" />

The newly generated 3'OH groups disrupt the host DNA's [[phosphodiester linkage]]s through SN2-type nucleophilic attack.<ref name=":2" /> 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.<ref name=":2" /><ref name=":3" />

=== Antiretroviral therapy ===
In November 2005, data from a [[Clinical trial|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 ==
{{Reflist|30em}}

== Further reading ==
{{refbegin}}
* {{cite journal | vauthors = Maertens GN, Engelman AN, Cherepanov P | title = Structure and function of retroviral integrase | journal = Nature Reviews. Microbiology | volume = 20 | issue = 1 | pages = 20–34 | date = January 2022 | pmid = 34244677 | doi = 10.1038/s41579-021-00586-9 | pmc = 8671357 | s2cid = 235787691 }} <!-- Token is public from Nature themselves: https://twitter.com/naturerevmicro/status/1413461830056415234 -->
{{refend}}

== External links ==
* PDB-101 Molecule of the Month: [https://pdb101.rcsb.org/motm/135 135 HIV Integrase]
* {{MeshName|Integrases}}

{{Phosphotransferases}}
{{Viral proteins}}

[[Category:Virology]]
[[Category:Enzymes]]
[[Category:Viral enzymes]]