1asu

Current revision

AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 2% PEG 400, 2M AMMONIUM SULFATE, HEPES PH 7.5

Structural highlights

1asu is a 1 chain structure with sequence from Avian sarcoma virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POL_RSVSB Capsid protein p27: Self-associates to form the irregular polyhedron core composed of hexamers and pentamers, that encapsulates the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro. Binds to inositol hexakisphosphate (IP6), which allows the assembly of the polyhedral capsid.[UniProtKB:P03322] Plays a role in the oligomerization of the Gag polyprotein and in the stabilization of the immature particle. Essential layering element during tube assembly. Allows the cooperative binging of Gag to the host plasma membrane.[UniProtKB:P03322] Binds strongly to viral nucleic acids and promotes their packaging (By similarity). Plays a role in the maturation-stabilization of the viral dimeric RNA via highly structured zinc-binding motifs (By similarity).[UniProtKB:P03322][UniProtKB:P0C776] The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275] Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions (PubMed:9218451). This recombination event is an essential step in the viral replication cycle. Has a strong preference for using the 3'-OH at the viral DNA end as a nucleophile.[UniProtKB:P03354]^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Bujacz G, Alexandratos J, Wlodawer A, Merkel G, Andrake M, Katz RA, Skalka AM. Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. J Biol Chem. 1997 Jul 18;272(29):18161-8. PMID:9218451

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1asu"

@@ Line 1: / Line 1: @@
-[[Image:1asu.gif|left|200px]]<br /><applet load="1asu" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1asu, resolution 1.70&Aring;" />
-'''AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 2% PEG 400, 2M AMMONIUM SULFATE, HEPES PH 7.5'''<br />
-==Overview==
+==AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 2% PEG 400, 2M AMMONIUM SULFATE, HEPES PH 7.5==
-Retroviral integrase (IN) functions to insert retroviral DNA into the host cell chromosome in a highly coordinated manner. IN catalyzes two biochemically separable reactions: processing of the viral DNA ends and joining of these ends to the host DNA. Previous studies suggested that these two reactions are chemically similar and are carried out by a single active site that is characterized by a highly conserved constellation of carboxylate residues, the D,D(35)E motif. We report here the crystal structure of the isolated catalytic domain of avian sarcoma virus (ASV) IN, solved using multiwavelength anomalous diffraction data for a selenomethionine derivative and refined at 1.7 A resolution. The protein is a crystallographic dimer with each monomer featuring a five-stranded mixed beta-sheet region surrounded by five alpha-helices. Based on the general fold and the arrangement of catalytic carboxylate residues, it is apparent that ASV IN is a member of a superfamily of proteins that also includes two types of nucleases, RuvC and RNase H. The general fold and the dimer interface are similar to those of the analogous domain of HIV-1 IN, whose crystal structure has been determined at 2.5 A resolution. However, the ASV IN structure is more complete in that all three critical carboxylic acids, Asp64, Asp121 and Glu157, are ordered. The ordered active site and the considerably higher resolution of the present structure are all important to an understanding of the mechanism of retroviral DNA integration, as well as for designing antiviral agents that may be effective against HIV.
+<StructureSection load='1asu' size='340' side='right'caption='[[1asu]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1asu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_sarcoma_virus Avian sarcoma virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ASU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ASU FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1asu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1asu OCA], [https://pdbe.org/1asu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1asu RCSB], [https://www.ebi.ac.uk/pdbsum/1asu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1asu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POL_RSVSB POL_RSVSB] Capsid protein p27: Self-associates to form the irregular polyhedron core composed of hexamers and pentamers, that encapsulates the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro. Binds to inositol hexakisphosphate (IP6), which allows the assembly of the polyhedral capsid.[UniProtKB:P03322]  Plays a role in the oligomerization of the Gag polyprotein and in the stabilization of the immature particle. Essential layering element during tube assembly. Allows the cooperative binging of Gag to the host plasma membrane.[UniProtKB:P03322]  Binds strongly to viral nucleic acids and promotes their packaging (By similarity). Plays a role in the maturation-stabilization of the viral dimeric RNA via highly structured zinc-binding motifs (By similarity).[UniProtKB:P03322][UniProtKB:P0C776]  The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]  Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions (PubMed:9218451). This recombination event is an essential step in the viral replication cycle. Has a strong preference for using the 3'-OH at the viral DNA end as a nucleophile.[UniProtKB:P03354]<ref>PMID:9218451</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/as/1asu_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1asu ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-ASU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Avian_sarcoma_virus Avian sarcoma virus] with <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ASU OCA].
+*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
+== References ==
-==Reference==
+<references/>
-High-resolution structure of the catalytic domain of avian sarcoma virus integrase., Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM, J Mol Biol. 1995 Oct 20;253(2):333-46. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7563093 7563093]
+__TOC__
+</StructureSection>
 [[Category: Avian sarcoma virus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Alexandratos, J.]]
+[[Category: Alexandratos J]]
-[[Category: Bujacz, G.]]
+[[Category: Bujacz G]]
-[[Category: Jaskolski, M.]]
+[[Category: Jaskolski M]]
-[[Category: Wlodawer, A.]]
+[[Category: Wlodawer A]]
-[[Category: EPE]]
-[[Category: dna integration]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:47:56 2008''