1vse

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(New page: 200px<br /><applet load="1vse" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vse, resolution 2.20&Aring;" /> '''ASV INTEGRASE CORE D...)
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[[Image:1vse.gif|left|200px]]<br /><applet load="1vse" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1vse, resolution 2.20&Aring;" />
 
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'''ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM'''<br />
 
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==Overview==
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==ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM==
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BACKGROUND: Members of the structurally-related superfamily of enzymes, that includes RNase H, RuvC resolvase, MuA transposase, and retroviral, integrase require divalent cations for enzymatic activity. So far, cation, positions are reported in the X-ray crystal structures of only two of, these proteins, E. coli and human immunodeficiency virus 1 (HIV-1) RNase, H. Details of the placement of metal ions in the active site of retroviral, integrases are necessary for the understanding of the catalytic mechanism, of these enzymes. RESULTS: The structure of the enzymatically active, catalytic domain (residues 52-207) of avian sarcoma virus integrase (ASV, IN) has been solved in the presence of divalent cations (Mn2+ or Mg2+), at, 1.7-2.2 A resolution. A single ion of either type interacts with the, carboxylate groups of the active site aspartates and uses four water, molecules to complete its octahedral coordination. The placement of the, aspartate side chains and metal ions is very similar to that observed in, the RNase H members of this superfamily; however, the conformation of the, catalytic aspartates in the active site of ASV IN differs significantly, from that reported for the analogous residues in HIV-1 IN. CONCLUSIONS:, Binding of the required metal ions does not lead to significant structural, modifications in the active site of the catalytic domain of ASV IN. This, indicates that at least one metal-binding site is preformed in the, structure, and suggests that the observed constellation of the acidic, residues represents a catalytically competent active site. Only a single, divalent cation was observed even at extremely high concentrations of the, metals. We conclude that either only one metal ion is needed for, catalysis, or that a second metal-binding site can only exist in the, presence of substrate and/or other domains of the protein. The unexpected, differences between the active sites of ASV IN and HIV-1 IN remain, unexplained; they may reflect the effects of crystal contacts on the, active site of HIV-1 IN, or a tendency for structural polymorphism.
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<StructureSection load='1vse' size='340' side='right'caption='[[1vse]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1vse]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rous_sarcoma_virus_(strain_Schmidt-Ruppin) Rous sarcoma virus (strain Schmidt-Ruppin)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VSE FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vse OCA], [https://pdbe.org/1vse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vse RCSB], [https://www.ebi.ac.uk/pdbsum/1vse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vse ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/1vse_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1vse ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1VSE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rous_sarcoma_virus Rous sarcoma virus] with EPE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VSE OCA].
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*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
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== References ==
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==Reference==
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<references/>
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The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations., Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM, Structure. 1996 Jan 15;4(1):89-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8805516 8805516]
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__TOC__
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[[Category: Rous sarcoma virus]]
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</StructureSection>
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Alexandratos, J.]]
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[[Category: Alexandratos J]]
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[[Category: Bujacz, G.]]
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[[Category: Bujacz G]]
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[[Category: Jaskolski, M.]]
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[[Category: Jaskolski M]]
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[[Category: Wlodawer, A.]]
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[[Category: Wlodawer A]]
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[[Category: EPE]]
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[[Category: endonuclease]]
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[[Category: hydrolase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:07:26 2007''
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Current revision

ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM

PDB ID 1vse

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