3fiv

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(New page: 200px<br /><applet load="3fiv" size="450" color="white" frame="true" align="right" spinBox="true" caption="3fiv, resolution 1.85&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:3fiv.gif|left|200px]]<br /><applet load="3fiv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="3fiv, resolution 1.85&Aring;" />
 
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'''CRYSTAL STRUCTURE OF FELINE IMMUNODEFICIENCY VIRUS PROTEASE COMPLEXED WITH A SUBSTRATE'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF FELINE IMMUNODEFICIENCY VIRUS PROTEASE COMPLEXED WITH A SUBSTRATE==
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Crystal structures of complexes of a D30N mutant of feline, immunodeficiency virus protease (FIV PR) complexed with a statine-based, inhibitor (LP-149), as well as with a substrate based on a modification of, this inhibitor (LP-149S), have been solved and refined at resolutions of, 2.0 and 1.85 A, respectively. Both the inhibitor and the substrate are, bound in the active site of the mutant protease in a similar mode, which, also resembles the mode of binding of LP-149 to the native protease. The, carbonyl oxygen of the scissile bond in the substrate is not hydrated and, is located within the distance of a hydrogen bond to an amido nitrogen, atom from one of the two asparagines in the active site of the enzyme. The, nitrogen atom of the scissile bond is 3.25 A from the conserved water, molecule (Wat301). A model of a tetrahedral intermediate bound to the, active site of the native enzyme was built by considering the interactions, observed in all three crystal structures of FIV PR. Molecular dynamics, simulations of this model bound to native wild-type FIV PR were carried, out, to investigate the final stages of the catalytic mechanism of, aspartic proteases.
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<StructureSection load='3fiv' size='340' side='right'caption='[[3fiv]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3fiv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Feline_immunodeficiency_virus Feline immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FIV 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]] 1.85&#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=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALN:NAPHTHALEN-2-YL-3-ALANINE'>ALN</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3fiv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fiv OCA], [https://pdbe.org/3fiv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fiv RCSB], [https://www.ebi.ac.uk/pdbsum/3fiv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fiv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/POL_FIVPE POL_FIVPE] During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
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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/fi/3fiv_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=3fiv ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Crystal structures of complexes of a D30N mutant of feline immunodeficiency virus protease (FIV PR) complexed with a statine-based inhibitor (LP-149), as well as with a substrate based on a modification of this inhibitor (LP-149S), have been solved and refined at resolutions of 2.0 and 1.85 A, respectively. Both the inhibitor and the substrate are bound in the active site of the mutant protease in a similar mode, which also resembles the mode of binding of LP-149 to the native protease. The carbonyl oxygen of the scissile bond in the substrate is not hydrated and is located within the distance of a hydrogen bond to an amido nitrogen atom from one of the two asparagines in the active site of the enzyme. The nitrogen atom of the scissile bond is 3.25 A from the conserved water molecule (Wat301). A model of a tetrahedral intermediate bound to the active site of the native enzyme was built by considering the interactions observed in all three crystal structures of FIV PR. Molecular dynamics simulations of this model bound to native wild-type FIV PR were carried out, to investigate the final stages of the catalytic mechanism of aspartic proteases.
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==About this Structure==
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Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor.,Laco GS, Schalk-Hihi C, Lubkowski J, Morris G, Zdanov A, Olson A, Elder JH, Wlodawer A, Gustchina A Biochemistry. 1997 Sep 2;36(35):10696-708. PMID:9271500<ref>PMID:9271500</ref>
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3FIV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Feline_immunodeficiency_virus Feline immunodeficiency virus] with SO4 and ACE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3FIV OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor., Laco GS, Schalk-Hihi C, Lubkowski J, Morris G, Zdanov A, Olson A, Elder JH, Wlodawer A, Gustchina A, Biochemistry. 1997 Sep 2;36(35):10696-708. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9271500 9271500]
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</div>
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[[Category: Feline immunodeficiency virus]]
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<div class="pdbe-citations 3fiv" style="background-color:#fffaf0;"></div>
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[[Category: HIV-1 retropepsin]]
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[[Category: Single protein]]
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[[Category: Gustchina, A.]]
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[[Category: Lubkowski, J.]]
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[[Category: Schalk-Hihi, C.]]
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[[Category: Wlodawer, A.]]
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[[Category: Zdanov, A.]]
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[[Category: ACE]]
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[[Category: SO4]]
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[[Category: aspartic protease]]
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[[Category: complex (acid proteinase/substrate)]]
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[[Category: retroviral protease]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:43:40 2007''
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==See Also==
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*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Feline immunodeficiency virus]]
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[[Category: Large Structures]]
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[[Category: Gustchina A]]
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[[Category: Lubkowski J]]
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[[Category: Schalk-Hihi C]]
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[[Category: Wlodawer A]]
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[[Category: Zdanov A]]

Current revision

CRYSTAL STRUCTURE OF FELINE IMMUNODEFICIENCY VIRUS PROTEASE COMPLEXED WITH A SUBSTRATE

PDB ID 3fiv

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