1f7q: Difference between revisions

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-[[Image:1f7q.gif|left|200px]]<br /><applet load="1f7q" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1f7q, resolution 2.26&Aring;" />
-'''CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.'''<br />
-==Overview==
+==CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.==
-dUTP pyrophosphatase (dUTPase) cleaves the alpha-beta phosphodiester of dUTP to form pyrophosphate and dUMP, preventing incorporation of uracil into DNA and providing the substrate for thymine synthesis. Seven crystal structures of feline immunodeficiency virus (FIV) dUTPase in three crystal forms have been determined, including complexes with substrate (dUTP), product (dUMP) or inhibitor (dUDP) bound. The native enzyme has been refined at 1.40 A resolution in a hexagonal crystal form and at 2.3 A resolution in an orthorhombic crystal form. In the dUDP complex in a cubic crystal form refined at 2.5 A resolution, the C-terminal conserved P-loop motif is fully ordered. The analysis defines the roles of five sequence motifs in interaction with uracil, deoxyribose and the alpha-, beta- and gamma-phosphates. The enzyme utilizes adaptive recognition to bind the alpha- and beta-phosphates. In particular, the alpha-beta phosphodiester adopts an unfavorable eclipsed conformation in the presence of the P-loop. This conformation may be relevant to the mechanism of alpha-beta phosphodiester bond cleavage.
+<StructureSection load='1f7q' size='340' side='right'caption='[[1f7q]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1f7q]] is a 3 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=1F7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7Q FirstGlance]. <br>
-F7Q 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 <scene name='pdbligand=DUT:'>DUT</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7Q OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.26&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7q OCA], [https://pdbe.org/1f7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7q RCSB], [https://www.ebi.ac.uk/pdbsum/1f7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7q ProSAT]</span></td></tr>
-Structures of feline immunodeficiency virus dUTP pyrophosphatase and its nucleotide complexes in three crystal forms., Prasad GS, Stura EA, Elder JH, Stout CD, Acta Crystallogr D Biol Crystallogr. 2000 Sep;56(Pt 9):1100-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10957629 10957629]
+</table>
+== Function ==
+[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.
+== 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/f7/1f7q_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=1f7q ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Feline immunodeficiency virus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: dUTP diphosphatase]]
+[[Category: Elder JH]]
-[[Category: Elder, J H.]]
+[[Category: Prasad GS]]
-[[Category: Prasad, G S.]]
+[[Category: Stout CD]]
-[[Category: Stout, C D.]]
+[[Category: Stura EA]]
-[[Category: Stura, E A.]]
-[[Category: DUT]]
-[[Category: eight stranded beta barrel protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:35:44 2008''