1vse

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[[Image:1vse.gif|left|200px]]
 
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==ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM==
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The line below this paragraph, containing "STRUCTURE_1vse", creates the "Structure Box" on the page.
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<StructureSection load='1vse' size='340' side='right'caption='[[1vse]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_1vse| PDB=1vse | SCENE= }}
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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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'''ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM'''
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==See Also==
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*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
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== References ==
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==Overview==
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<references/>
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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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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1VSE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rous_sarcoma_virus Rous sarcoma virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VSE OCA].
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[[Category: Alexandratos J]]
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[[Category: Bujacz G]]
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==Reference==
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[[Category: Jaskolski M]]
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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://www.ncbi.nlm.nih.gov/pubmed/8805516 8805516]
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[[Category: Wlodawer A]]
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[[Category: Rous sarcoma virus]]
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[[Category: Single protein]]
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[[Category: Alexandratos, J.]]
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[[Category: Bujacz, G.]]
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[[Category: Jaskolski, M.]]
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[[Category: Wlodawer, A.]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:51:56 2008''
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ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM

PDB ID 1vse

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