IN - Integrase

HIV IN mediates the insertion of viral DNA into the host genome.




PDB-2ITG: HIV-1 (isolate UNKNOWN) Integrase - produced using SwissModel/SPDBV/POVray

Key web links:
ViralZone: HIV-1, HIV replication cycle, HIV resource
PDB: 2ITG (HIV-1 Integrase)
UniProt: P04585 (HIV-1 HXB2 POL)
Chime Tutorial: Online Macromolecular Museum
HIV-1/Human Protein Interaction DB: HIV-1 Pol
Los Alamos HIV structure DB: Integrase
EMBL: K03455 [EMBL/GenBank/DDBJ]


Isoforms:

  • p31 (288 amino acids)


Cleavage sites:


Function:

  • Viral enzyme.
  • Catalyses viral DNA integration into the host chromosome .
  • Exonuclease activity trims two nucleotides from each 3'-end of the linear DNA duplux .
  • Double-stranded endonuclease activity cleaves the host DNA at the integration site .
  • Ligase activity generates a single covalent linkage at each end of viral DNA .
  • Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.
  • The first step is site-specific endonucleolytic cleavage of the 30-ends of the viral DNA.
  • Secondly, it participates in the assembly of the pre-integration complex (PIC) on the ends of the viral DNA, which migrates into the host nucleus.
  • Lastly, integrase catalyzes the insertion of the viral DNA into host chromosomal DNA (strand transfer step).

Localization:

  • Virion
  • Cell nucleus
  • Host cytoplasm

Additional Information:

  • Late timing of expression.
  • After integration, cellular enzymes repair the integration site.
  • No exogenous energy source (ie. ATP) is required for integration.
  • Accessibility of chromosomal DNA, not a specific DNA sequence, influences the site of integration .
  • DNA kinking are "hot-spots" for integration in in vitro studies .
  • Integration into regions of open, transcriptionally active, chromatin may facilitate expression of viral proteins.
  • Non-integrated proviral DNA is expressed inefficiently .

Integrase Function & Host-Virus Protein Interactions:[TOP]




Interactions highlighted in the image:


Potential interactions (not in the image):



Genomic Location & Protein Sequence: [TOP]

HIV-1 (HXB2):

          10         20         30         40         50         60         70	       80         90        100
| | | | | | | | | |
FLDGIDKAQD EHEKYHSNWR AMASDFNLPP VVAKEIVASC DKCQLKGEAM HGQVDCSPGI WQLDCTHLEG KVILVAVHVA SGYIEAEVIP AETGQETAYF
110 120 130 140 150 160 170 180 190 200
| | | | | | | | | |
LLKLAGRWPV KTIHTDNGSN FTGATVRAAC WWAGIKQEFG IPYNPQSQGV VESMNKELKK IIGQVRDQAE HLKTAVQMAV FIHNFKRKGG IGGYSAGERI
210 220 230 240 250 260 270 280 288
| | | | | | | | |
VDIIATDIQT KELQKQITKI QNFRVYYRDS RNPLWKGPAK LLWKGEGAVV IQDNSDIKVV PRRKAKIIRD YGKQMAGDDC VASRQDED
[download in fasta format]

Length: 288 amino acids
Molecular Weight: 32166 Da
Theoretical pI: 8.16
Position relative to Pol protein: 716 - 1003

Protein Domains/Folds/Motifs: [TOP]

InterPro signature for Retroviral Integrase, C-terminal - IPR001037

InterPro signature for Integrase, catalytic domain - IPR001584


Secondary Structure prediction:

Antigenic Sites - EMBOSS:





Predicted Motifs: Printer-friendly version

N-glycosylation:
N-myristoylation:
Amidation:
Protein kinase C:
Casein kinase II:
Tyrosine kinase:
cAMP / cGMP kinase:
Cell attachment motif:
Asp Protease motif:
Asp Prot Retro motif:
Cysteine-rich Region:
Tryptophan-rich Region:
Zinc-finger CCHC motif:
Leucine Zipper motif:

HIV Antiretrovirals and Drug Resistance Mutations: [TOP]

See Stanford University HIV Drug Resistance Database, which contains information different HIV-1 subtypes and CRFs 01 and 02


See a recent review on HIV-1 drug resistance and subtypes, with special focus on HIV-1 subtype C, the most prevalent HIV-1 strain in the world


See ViralZone HIV Drug Pages


Mechanism of Action:


Integrase mediates the formation of newly reverse transcribed viral DNA into a stable complex known as the pre-integration complex (PIC). Once this complex has been formed, integrase facilitates host nucleus entry and mediates the integration of the viral DNA into the host genome. Raltegravir is an integrase inhibitor (INI) that interacts with the divalent metals within the active site of integrase, inhibiting the insertion of the viral DNA into the host genome. Elvitegravir also inhibits the strand-transfer process of HIV integration . Dolutegravir is a second-generation INI that has recently been approved .


Drug Resistance Mutations:


INI:
Position Mutation Additional Information Drugs Affected Reference
T66 I Mutation is associated with a large decrease in drug susceptibility (>5-10 fold). Elvitegravir
D McColl, HIV Drug Resistance Workshop (2007)
E92 Q Mutation is associated with a large decrease in drug susceptibility (>5-10 fold). Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
F121 Y Mutation is associated with a large decrease in drug susceptibility (>5-10 fold). Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
E138 A, K Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
G140 A, S Mutations are associated with a large decrease in drug susceptibility (>5-10 fold). Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
Y143 R, C, H Y143R/C mutations are associated with a large decrease in drug susceptibility (>5-10 fold). Raltegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
S147 G Mutation is associated with a large decrease in Elvitegravir susceptibility (>5-10 fold). Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
Q148 H, R, K Mutations are associated with a large decrease in drug susceptibility (>5-10 fold). Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
S153 Y Elvitegravir
D McColl, HIV Drug Resistance Workshop (2007)
N155 H, S N155H mutation is associated with a large decrease in drug susceptibility (>5-10 fold). Raltegravir, Elvitegravir
D Hazuda, HIV Drug Resistance Workshop (2007)
D McColl, HIV Drug Resistance Workshop (2007)
R263 K Elvitegravir
D McColl, HIV Drug Resistance Workshop (2007)
Primary and Secondary Database Entries: [TOP]

Identifiers:



ViralZone: HIV-1, HIV replication cycle, HIV resource
PDB/MMDB: Search for HIV-1 & Integrase

UniProt: P04585 (HIV-1 HXB2 POL)
EC: NONE
EMBL: K03455; AAB50259.1 [EMBL/GenBank/DDBJ]

InterPro: IPR001037 - Integrase C-terminal family
IPR001584 - Integrase catalytic domain
IPR003308 - Integrase N-terminal zinc-binding domain
Pfam: PF00552 / PF00665 / PF02022
Prints: none
SCOP: SSF46919 (N-terminus) Zn-binding domain / SSF53098 Ribonuclease H-like protein
SSF50122 (C-terminus) DNA-binding domain
BLOCKS: P04585
Prosite: P04585
ProtoNet: P04585
Database of Interacting Proteins: P04585
ModBase: P04585
HIV-1/Human Protein Interaction DB: HIV-1 Pol
HIV-1 Sequence Database Los Alamos HIV Sequence Database

PDB:




Reviews and References: [TOP]


Cite the resource by citing the following paper:
Doherty R et al. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology (2005), 9;2(1):18.

1 - HIV Sequence Compendium 2000
Kuiken CL, Foley B, Hahn B, Korber B, Marx PA, McCutchan F, Mellors JW, Mullins JI, Sodroski J, Wolinksy S.
Theoretical Biol. & Biophys. Group, Los Alamos Nat Lab, LA-UR 01-3860 [Read it online: Compendium]
2 - Retroviruses
Coffin JM, Hughes SH, Varmus HE.
CD-ROM ed. (2002) Cold Spring Harbor Laboratory Press [Read it online: NCBI Bookshelf]
3 - Molecular Characteristics of HIV-1 Subtype C Viruses from KwaZulu-Natal, South Africa:
Implications for Vaccine and Antiretroviral Control Strategies.
Gordon M, De Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S.
Journal of Virology 77(4): 2587-2599 (2003) [pubmed: 12551997]
4 - Retroviral DNA integration directed by HIV integration protein in vitro.
Bushman FD, Fujiwara T, Craigie R.
Science 249: 1555-1558 (1990) [pubmed: 2171144]
5 - Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target
site selection.
Pryciak PM, Varmus HE.
Cell 69: 769-780 (1992) [pubmed: 1317268]
6 - Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion
within the nucleosome core.
Pruss D, Bushman FD, Wolffe AP.
Proc Natl Acad Sci USA 91: 5913-5917 (1994) [pubmed: 8016088]
7 - Human immunodeficiency virus type 1 integrase: Effects of mutations on viral ability to integrate,
direct viral gene expression from unintegrated viral DNA templates, and sustain viral propagation in primary cells.
Wiskerchen M, Muesing MA.
J Virol 69: 376-386 (1995) [pubmed: 7983732]
8 - [HIV Integrase Review - pdb:1K6Y] Structure of a two-domain fragment of HIV-1 integrase:
implications for domain organization in the intact protein.
Wang JY, Ling H, Yang W, Craigie R.
EMBO J 20(24): 7333-7343 (2001) [pubmed: 11743009]
9 - [Drug Resistant Mutations] Molecular Dynamics Studies of the Wild-Type and Double Mutant HIV-1
Integrase Complexed with the 5CITEP Inhibitor: Mechanism for Inhibition and Drug Resistance.
Barreca ML, Lee KW, Chimirri A, Briggs JM.
Biophys J 84(3): 1450-1463 (2003) [pubmed: 12609852]
10 - [Integrase forms multimers] HIV-1 integrase forms stable tetramers and associates with
LEDGF/p75 protein in human cells.
Cherepanov P, Maertens G, Proost P, Devreese B, Van Beeumen J, Engelborghs Y, De Clercq E, Debyser Z.
J Biol Chem 278(1): 372-81 (2003) [pubmed: 12407101]
11 - [EBR28 - peptide inhibitor of Integrase] A novel short peptide is a specific inhibitor of the
human immunodeficiency virus type 1 integrase.
de Soultrait VR, Caumont A, Parissi V, Morellet N, Ventura M, Lenoir C, Litvak S, Fournier M, Roques B.
J Mol Biol 318(1): 45-58 (2002) [pubmed: 12054767]
 12 - [Human Rad18 DNA damage/repair enzyme - stabilizes Integrase]
Interaction of HIV-1 integrase with DNA repair protein hRad18.
Mulder LC, Chakrabarti LA, Muesing MA.
J Biol Chem 277(30): 27489-27493 (2002) [pubmed: 12016221]
13 - Integrase and integration: biochemical activities of HIV-1 integrase.
Delelis O, Carayon K, Sab A, Deprez E, Mouscadet JF.
Retrovirology 17;5:114 (2008) [pubmed: 19091057]
14 - The lentiviral integrase binding protein LEDGF/p75 and HIV-1 replication.
Engelman A, Cherepanov P.
PLoS Pathog. 4(3):e1000046 (2008) [pubmed: 18369482]
15 - Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5.
Kalpana GV, Marmon S, Wang W, Crabtree GR, Goff SP.
Science 266(5193):2002-6 (1994) [pubmed: 7801128]
16 - Importin alpha3 interacts with HIV-1 integrase and contributes to HIV-1 nuclear import and replication.
Ao Z, Danappa Jayappa K, Wang B, Zheng Y, Kung S, Rassart E, Depping R, Kohler M, Cohen EA, Yao X.
J Virol. 84(17):8650-63 (2010) [pubmed: 20554775]
17 - Interaction of human immunodeficiency virus type 1 integrase with cellular nuclear import receptor importin 7 and its impact on viral replication.
Ao Z, Huang G, Yao H, Xu Z, Labine M, Cochrane AW, Yao X.
J Biol Chem. 282(18):13456-67 (2007) [pubmed: 17360709]
18 - Functional role of HIV-1 virion-associated uracil DNA glycosylase 2 in the correction of G:U mispairs to G:C pairs.
Priet S, Navarro JM, Gros N, Querat G, Sire J.
J Biol Chem. 278(7):4566-71 (2003) [pubmed: 12458223]
19 - Interaction of the HIV-1 intasome with transportin 3 protein (TNPO3 or TRN-SR2).
Larue R, Gupta K, Wuensch C, Shkriabai N, Kessl JJ, Danhart E, Feng L, Taltynov O, Christ F, Van Duyne GD, Debyser Z, Foster MP, Kvaratskhelia M.
J Biol Chem. 287(41):34044-58 (2012) [pubmed: 22872640]
20 - Integrase interacts with nucleoporin NUP153 to mediate the nuclear import of human immunodeficiency virus type 1.
Woodward CL, Prakobwanakit S, Mosessian S, Chow SA.
J Virol. 83(13):6522-33 (2009) [pubmed: 19369352]
21 - Contribution of host nucleoporin 62 in HIV-1 integrase chromatin association and viral DNA integration.
Ao Z, Jayappa KD, Wang B, Zheng Y, Wang X, Peng J, Yao X.
J Biol Chem. 287(13):10544-55 (2012) [pubmed: 22308026]
22 - Augmentation of reverse transcription by integrase through an interaction with host factor, SIP1/Gemin2 Is critical for HIV-1 infection.
Nishitsuji H, Hayashi T, Takahashi T, Miyano M, Kannagi M, Masuda T.
PLoS One 4(11):e7825 (2009) [pubmed: 19915660]
23 - Elvitegravir: a review of its use in adults with HIV-1 infection.
Deeks ED.
Drugs 74(6):687-97 (2014) [pubmed: 24671908]
24 - Dolutegravir: an exciting new kid on the block.
Blanco Arévalo JL, Whitlock GG.
Expert Opin Pharmacother. 15(4):573-82 (2014) [pubmed: 24446762]
25 - Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update.
Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, Kiuchi M, Heneine W, Kantor R, Jordan MR, Schapiro JM, Vandamme AM, Sandstrom P, Boucher CA, van de Vijver D, Rhee SY, Liu TF, Pillay D, Shafer RW.
PLoS One 4(3):e4724 (2009) [pubmed: 19266092]
26 - Mutations associated with failure of raltegravir treatment affect integrase sensitivity to the inhibitor in vitro.
Malet I, Delelis O, Valantin MA, Montes B, Soulie C, Wirden M, Tchertanov L, Peytavin G, Reynes J, Mouscadet JF, Katlama C, Calvez V, Marcelin AG.
Antimicrob Agents Chemother. 52(4):1351-8 (2008) [pubmed: 18227187]



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