Integrase - Revision history

Michal Harel at 10:50, 4 September 2018

2018-09-04T10:50:00Z

← Older revision		Revision as of 10:50, 4 September 2018
Line 145:		Line 145:
	***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]		***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
	</StructureSection>		</StructureSection>
	==3D structures of integrase see [[Retroviral ~~integrase~~]]==		==3D structures of integrase see [[Retroviral Integrase]]==

	[[Category:Topic Page]][[Category:PDBe]]		[[Category:Topic Page]][[Category:PDBe]]

Michal Harel at 10:48, 4 September 2018

2018-09-04T10:48:39Z

@@ Line 145: / Line 145: @@
 ***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
 </StructureSection>
-==3D structures of integrase==
+==3D structures of integrase see [[Retroviral integrase]]==
 [[Category:Topic Page]][[Category:PDBe]]

Michal Harel at 09:36, 4 September 2018

2018-09-04T09:36:29Z

← Older revision		Revision as of 09:36, 4 September 2018
Line 144:		Line 144:
	***1.45 A resolution		***1.45 A resolution
	***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]		***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
			</StructureSection>
	==3D structures of integrase==		==3D structures of integrase==

Michal Harel at 09:33, 4 September 2018

2018-09-04T09:33:43Z

← Older revision		Revision as of 09:33, 4 September 2018
Line 177:		Line 177:
	*Integrase complex		*Integrase complex

	**[[2a3v – Rec INTI4+DNA – Vibrio cholera<br />		**[[2a3v]] – Rec INTI4+DNA – ''Vibrio cholera''<br />
	**[[1z19, 1z1b, 1z1g, 1p7d – EpLamInt catalytic core domain+DNA<br />		**[[1z19]], [[1z1b]], [[1z1g]], [[1p7d]] – EpLamInt catalytic core domain+DNA<br />
	**[[1p4e, 1m6x – yFLP (mutant)+DNA – yeast<br />		**[[1p4e]], 1m6x]] – yFLP (mutant)+DNA – yeast<br />
	**[[1flo - yFLP +DNA<br />		**[[1flo]] - yFLP +DNA<br />
	**[[2wcc]] – INT DBD+ DNA – Enterobacteria phage - NMR<br />		**[[2wcc]] – INT DBD+ DNA – Enterobacteria phage - NMR<br />
	**[[5j0n]] – INT + ATTP + ATTB + integration host factor + excisionase - Cryo EM<br />		**[[5j0n]] – INT + ATTP + ATTB + integration host factor + excisionase - Cryo EM<br />

Michal Harel at 09:32, 4 September 2018

2018-09-04T09:32:27Z

@@ Line 144: / Line 144: @@
 ***1.45 A resolution
 ***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
 [[Category:Topic Page]][[Category:PDBe]]

Michal Harel at 11:21, 3 February 2016

2016-02-03T11:21:04Z

← Older revision		Revision as of 11:21, 3 February 2016
Line 1:		Line 1:
	<StructureSection load='3fx5' size='340' side='right' caption='~~The best structure for Integrase shown:~~ 3fx5' scene=''>		<StructureSection load='3fx5' size='340' side='right' caption='HIV protease complex with inhibitor and glycerol (PDB code [[3fx5]])' scene=''>
	Best example is PDB entry [[3fx5]] and is shown in the viewer.<br>		Best example is PDB entry [[3fx5]] and is shown in the viewer.<br>
	Molecule Integrase, also known as Integrase, p2B, p10, Capsid protein p27, p4, p3, Reverse transcriptase beta-subunit, Protease p15, Nucleocapsid protein p12, Reverse transcriptase alpha-subunit, RT-alpha, p2A, RT-beta, Gag-Pro-Pol polyprotein, pp32, Matrix protein p19, IN, Matrix protein p17, Transframe peptide, Reverse transcriptase/ribonuclease H, Pr160Gag-Pol, Spacer peptide 1, p2, Exoribonuclease H, p6*, Gag-Pol polyprotein, Nucleocapsid protein p7, p15, Retropepsin, p6-pol, p66 RT, Protease, PR, CA, TF, NC, SP1, Capsid protein p24, MA, p51 RT, Ribonuclease H, Protease/Reverse transcriptase, Pro-Pol polyprotein, Pr125Pol, Protease/Reverse transcriptase/ribonuclease H, RNase H, p87Pro-RT-RNaseH, p42In, p65Pro-RT, INT, Pol polyprotein, dUTPase, RT, Deoxyuridine 5'-triphosphate nucleotidohydrolase, P72, Pr170Gag-Pol, p11, p2L, Capsid protein p26, Matrix protein p16, P119, Putative prophage integrase, Int protein, CP4-like integrase, Transposase from transposon Tn916, NC-pro, Pr160Gag-Pro-Pol, Nucleocapsid protein p15-pro, p1 and NC'.		Molecule Integrase, also known as Integrase, p2B, p10, Capsid protein p27, p4, p3, Reverse transcriptase beta-subunit, Protease p15, Nucleocapsid protein p12, Reverse transcriptase alpha-subunit, RT-alpha, p2A, RT-beta, Gag-Pro-Pol polyprotein, pp32, Matrix protein p19, IN, Matrix protein p17, Transframe peptide, Reverse transcriptase/ribonuclease H, Pr160Gag-Pol, Spacer peptide 1, p2, Exoribonuclease H, p6*, Gag-Pol polyprotein, Nucleocapsid protein p7, p15, Retropepsin, p6-pol, p66 RT, Protease, PR, CA, TF, NC, SP1, Capsid protein p24, MA, p51 RT, Ribonuclease H, Protease/Reverse transcriptase, Pro-Pol polyprotein, Pr125Pol, Protease/Reverse transcriptase/ribonuclease H, RNase H, p87Pro-RT-RNaseH, p42In, p65Pro-RT, INT, Pol polyprotein, dUTPase, RT, Deoxyuridine 5'-triphosphate nucleotidohydrolase, P72, Pr170Gag-Pol, p11, p2L, Capsid protein p26, Matrix protein p16, P119, Putative prophage integrase, Int protein, CP4-like integrase, Transposase from transposon Tn916, NC-pro, Pr160Gag-Pro-Pol, Nucleocapsid protein p15-pro, p1 and NC'.

PDBe: New page: Best example is PDB entry 3fx5 and is shown in the viewer.
Mo...

2015-09-15T20:23:20Z

New page: <StructureSection load='3fx5' size='340' side='right' caption='The best structure for Integrase shown: 3fx5' scene=''> Best example is PDB entry 3fx5 and is shown in the viewer.<br> Mo...

New page

<StructureSection load='3fx5' size='340' side='right' caption='The best structure for Integrase shown: 3fx5' scene=''>
Best example is PDB entry [[3fx5]] and is shown in the viewer.<br>
Molecule Integrase, also known as Integrase, p2B, p10, Capsid protein p27, p4, p3, Reverse transcriptase beta-subunit, Protease p15, Nucleocapsid protein p12, Reverse transcriptase alpha-subunit, RT-alpha, p2A, RT-beta, Gag-Pro-Pol polyprotein, pp32, Matrix protein p19, IN, Matrix protein p17, Transframe peptide, Reverse transcriptase/ribonuclease H, Pr160Gag-Pol, Spacer peptide 1, p2, Exoribonuclease H, p6*, Gag-Pol polyprotein, Nucleocapsid protein p7, p15, Retropepsin, p6-pol, p66 RT, Protease, PR, CA, TF, NC, SP1, Capsid protein p24, MA, p51 RT, Ribonuclease H, Protease/Reverse transcriptase, Pro-Pol polyprotein, Pr125Pol, Protease/Reverse transcriptase/ribonuclease H, RNase H, p87Pro-RT-RNaseH, p42In, p65Pro-RT, INT, Pol polyprotein, dUTPase, RT, Deoxyuridine 5'-triphosphate nucleotidohydrolase, P72, Pr170Gag-Pol, p11, p2L, Capsid protein p26, Matrix protein p16, P119, Putative prophage integrase, Int protein, CP4-like integrase, Transposase from transposon Tn916, NC-pro, Pr160Gag-Pro-Pol, Nucleocapsid protein p15-pro, p1 and NC'.
== Function ==
Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.Data source: Uniprot [http://www.uniprot.org/uniprot/P03367 P03367]<br>
==Catalytic Activity ==
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).Data source: Uniprot [http://www.uniprot.org/uniprot/P03367 P03367]<br>

== Disease ==

== Relevance ==

== Structural highlights ==
== Biological process ==
Is involved in the following biological processes:<br>
proteolysis<br>
DNA integration<br>
RNA-dependent DNA replication<br>
viral process<br>
dUTP metabolic process<br>
DNA recombination<br>
establishment of integrated proviral latency<br>
viral entry into host cell<br>
== In structures ==
Integrase is found in 1103 PDB entries<br>
*<b>Viruses</b> (1062 PDB entries): <br>
**<b>Human immunodeficiency virus 1</b> (550 PDB entries): <br>
***[[3fx5]] <div class="pdb-prints 3fx5"></div>
***Title: Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High Resolution X-ray Crystallography
***0.93 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%201%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>HIV-1 M:B_HXB2R</b> (71 PDB entries): <br>
***[[3kt5]] <div class="pdb-prints 3kt5"></div>
***Title: Crystal Structure of N88S mutant HIV-1 Protease
***1.801 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22HIV-1%20M:B_HXB2R%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 1 BH10</b> (69 PDB entries): <br>
***[[4zip]] <div class="pdb-prints 4zip"></div>
***Title: HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)
***1.11 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%201%20BH10%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)</b> (52 PDB entries): <br>
***[[3avj]] <div class="pdb-prints 3avj"></div>
***Title: Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site
***1.7 A resolution
***Other macromolecules also in this entry: LEDGF peptide..
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%201%20(NEW%20YORK-5%20ISOLATE)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>HIV-1 M:B_ARV2/SF2</b> (46 PDB entries): <br>
***[[4obj]] <div class="pdb-prints 4obj"></div>
***Title: Crystal Structure of Inactive HIV-1 Protease in Complex with the p1-p6 substrate variant (S451N)
***1.75 A resolution
***Other macromolecules also in this entry: Spacer peptide 2..
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22HIV-1%20M:B_ARV2/SF2%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 1 (BRU ISOLATE)</b> (45 PDB entries): <br>
***[[3vf7]] <div class="pdb-prints 3vf7"></div>
***Title: Crystal Structure of HIV-1 Protease Mutant L76V with novel P1'-Ligands GRL-02031
***1.3 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%201%20(BRU%20ISOLATE)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human spumaretrovirus</b> (44 PDB entries): <br>
***[[3oym]] <div class="pdb-prints 3oym"></div>
***Title: Crystal structure of the PFV N224H mutant intasome bound to manganese
***2.02 A resolution
***Other macromolecules also in this entry: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3'), DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3').
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20spumaretrovirus%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus</b> (41 PDB entries): <br>
***[[1kzk]] <div class="pdb-prints 1kzk"></div>
***Title: JE-2147-HIV Protease Complex
***1.09 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)</b> (16 PDB entries): <br>
***[[2wkz]] <div class="pdb-prints 2wkz"></div>
***Title: HIV-1 Protease Inhibitors Containing a Tertiary Alcohol in the Transition-State Mimic with Improved Cell-Based Antiviral Activity
***1.7 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%201%20(Z2/CDC-Z34%20ISOLATE)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Feline immunodeficiency virus</b> (13 PDB entries): <br>
***[[1fiv]] <div class="pdb-prints 1fiv"></div>
***Title: STRUCTURE OF AN INHIBITOR COMPLEX OF PROTEINASE FROM FELINE IMMUNODEFICIENCY VIRUS
***2.0 A resolution
***Other macromolecules also in this entry: FIV PROTEASE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2..
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Feline%20immunodeficiency%20virus%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 1 (BH5 ISOLATE)</b> (12 PDB entries): <br>
***[[3d20]] <div class="pdb-prints 3d20"></div>
***Title: Crystal structure of HIV-1 mutant I54V and inhibitor DARUNAVIA
***1.05 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%201%20(BH5%20ISOLATE)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Rous sarcoma virus (strain Schmidt-Ruppin)</b> (11 PDB entries): <br>
***[[1a5x]] <div class="pdb-prints 1a5x"></div>
***Title: ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3
***1.9 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Rous%20sarcoma%20virus%20(strain%20Schmidt-Ruppin)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 2 (ISOLATE ROD)</b> (8 PDB entries): <br>
***[[3ecg]] <div class="pdb-prints 3ecg"></div>
***Title: High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065
***1.18 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%202%20(ISOLATE%20ROD)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Avian sarcoma virus</b> (7 PDB entries): <br>
***[[1czb]] <div class="pdb-prints 1czb"></div>
***Title: ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES
***1.06 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Avian%20sarcoma%20virus%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Human immunodeficiency virus type 1 (CLONE 12)</b> (5 PDB entries): <br>
***[[1hxb]] <div class="pdb-prints 1hxb"></div>
***Title: HIV-1 proteinase complexed with RO 31-8959
***2.3 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Human%20immunodeficiency%20virus%20type%201%20(CLONE%2012)%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>HUMAN IMMUNODEFICIENCY VIRUS 1</b> (4 PDB entries): <br>
***[[2j9k]] <div class="pdb-prints 2j9k"></div>
***Title: Atomic-resolution Crystal Structure of Chemically-Synthesized HIV-1 Protease Complexed with Inhibitor MVT-101
***1.2 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22HUMAN%20IMMUNODEFICIENCY%20VIRUS%201%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Rous sarcoma virus - Prague C</b> (3 PDB entries): <br>
***[[4fw1]] <div class="pdb-prints 4fw1"></div>
***Title: Crystal structure of two-domain RSV INTEGRASE covalently linked with DNA
***1.86 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Rous%20sarcoma%20virus%20-%20Prague%20C%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Bovine immunodeficiency virus R29</b> (2 PDB entries): <br>
***[[3kkr]] <div class="pdb-prints 3kkr"></div>
***Title: Crystal structure of catalytic core domain of BIV integrase in crystal form I
***2.453 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Bovine%20immunodeficiency%20virus%20R29%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Streptomyces phage phiC31</b> (1 PDB entries): <br>
***[[4bqq]] <div class="pdb-prints 4bqq"></div>
***Title: Protein crystal structure of the N-terminal and recombinase domains of the Streptomyces temperate phage serine recombinase, fC31 integrase.
***2.15 A resolution
*<b>Bacteria</b> (10 PDB entries): <br>
**<b>Enterococcus faecalis</b> (4 PDB entries): <br>
***[[1bb8]] <div class="pdb-prints 1bb8"></div>
***Title: N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, 25 STRUCTURES
***N/A A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Enterococcus%20faecalis%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Yersinia pestis</b> (2 PDB entries): <br>
***[[3jtz]] <div class="pdb-prints 3jtz"></div>
***Title: Structure of the arm-type binding domain of HPI integrase
***1.3 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Yersinia%20pestis%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
**<b>Staphylococcus aureus subsp. aureus USA300_TCH1516</b> (1 PDB entries): <br>
***[[3nkh]] <div class="pdb-prints 3nkh"></div>
***Title: Crystal Structure of Integrase from MRSA strain Staphylococcus aureus
***2.502 A resolution
*<b>Eukaryota</b> (3 PDB entries): <br>
**<b>Homo sapiens</b> (3 PDB entries): <br>
***[[3ufn]] <div class="pdb-prints 3ufn"></div>
***Title: Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 in Complex with Saquinavir
***1.45 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22Integrase%22&!chimera:y Search for other PDB entries]
[[Category:Topic Page]][[Category:PDBe]]