1f7r - Revision history

OCA at 07:11, 7 February 2024

OCA — Wed, 07 Feb 2024 07:11:47 GMT

←Older revision		Revision as of 07:11, 7 February 2024
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	<StructureSection load='1f7r' size='340' side='right'caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1f7r' size='340' side='right'caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Fiv Fiv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f7r]] is a 1 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=1F7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7R FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=UDP:URIDINE-~~5~~-DIPHOSPHATE'>UDP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23]~~ </~~span~~></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=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [https://pdbe.org/1f7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [https://www.ebi.ac.uk/pdbsum/1f7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7r ProSAT]</span></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=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [https://pdbe.org/1f7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [https://www.ebi.ac.uk/pdbsum/1f7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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.	+	[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=1f7r ConSurf].		</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=1f7r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:10957629<ref>PMID:10957629</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1f7r" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Fiv~~]]	+	[[Category: Feline immunodeficiency virus]]
	[[Category: Large Structures]]		[[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: Eight stranded beta barrel protein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 09:47, 21 July 2021

OCA — Wed, 21 Jul 2021 09:47:19 GMT

←Older revision		Revision as of 09:47, 21 July 2021
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	<StructureSection load='1f7r' size='340' side='right'caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1f7r' size='340' side='right'caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Fiv Fiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F7R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fiv Fiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~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] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [~~http~~://pdbe.org/1f7r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f7r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7r ProSAT]</span></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=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [https://pdbe.org/1f7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [https://www.ebi.ac.uk/pdbsum/1f7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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.	+	[[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:54, 16 October 2019

OCA — Wed, 16 Oct 2019 07:54:56 GMT

←Older revision		Revision as of 07:54, 16 October 2019
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	==CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.==		==CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.==
-	<StructureSection load='1f7r' size='340' side='right' caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1f7r' size='340' side='right'caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fiv Fiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fiv Fiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Fiv]]		[[Category: Fiv]]
		+	[[Category: Large Structures]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
	[[Category: Elder, J H]]		[[Category: Elder, J H]]

OCA at 09:18, 27 December 2017

OCA — Wed, 27 Dec 2017 09:18:12 GMT

←Older revision		Revision as of 09:18, 27 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.==		==CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.==
	<StructureSection load='1f7r' size='340' side='right' caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1f7r' size='340' side='right' caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://pdbe.org/1f7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://pdbe.org/1f7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/1f7r_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/1f7r_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 16:04, 7 February 2016

OCA — Sun, 07 Feb 2016 16:04:27 GMT

←Older revision		Revision as of 16:04, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1f7r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:03, 10 September 2015

OCA — Thu, 10 Sep 2015 03:03:19 GMT

←Older revision		Revision as of 03:03, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1f7r' size='340' side='right' caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1f7r' size='340' side='right' caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://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=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fiv Fiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://pdbe.org/1f7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1f7r" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Feline immunodeficiency virus~~]]	+	[[Category: Fiv]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
	[[Category: Elder, J H]]		[[Category: Elder, J H]]

OCA at 16:30, 24 December 2014

OCA — Wed, 24 Dec 2014 16:30:02 GMT

←Older revision		Revision as of 16:30, 24 December 2014
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 00:05, 23 December 2014

OCA — Tue, 23 Dec 2014 00:05:08 GMT

←Older revision		Revision as of 00:05, 23 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://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=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://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=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	[[Category: Feline immunodeficiency virus]]		[[Category: Feline immunodeficiency virus]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
-	[[Category: Elder, J H.]]	+	[[Category: Elder, J H]]
-	[[Category: Prasad, G S.]]	+	[[Category: Prasad, G S]]
-	[[Category: Stout, C D.]]	+	[[Category: Stout, C D]]
-	[[Category: Stura, E A.]]	+	[[Category: Stura, E A]]
	[[Category: Eight stranded beta barrel protein]]		[[Category: Eight stranded beta barrel protein]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 13:51, 28 September 2014

OCA — Sun, 28 Sep 2014 13:51:37 GMT

←Older revision		Revision as of 13:51, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1f7r.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.==
		+	<StructureSection load='1f7r' size='340' side='right' caption='[[1f7r]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f7r]] is a 1 chain structure with sequence from [http://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=1F7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7R FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f7d\|1f7d]], [[1f7k\|1f7k]], [[1f7n\|1f7n]], [[1f7o\|1f7o]], [[1f7p\|1f7p]], [[1f7q\|1f7q]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7r RCSB], [http://www.ebi.ac.uk/pdbsum/1f7r PDBsum]</span></td></tr>
		+	<table>
		+	== 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/f7/1f7r_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1f7r\| PDB=1f7r \| SCENE= }}~~	+	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:10957629<ref>PMID:10957629</ref>

-	~~===CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~==About this Structure==~~	+	<references/>
-	~~[[1f7r]] is~~ a ~~1 chain structure with sequence from [http://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=1F7R OCA].~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010957629<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Feline immunodeficiency virus]]		[[Category: Feline immunodeficiency virus]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]

OCA: Protected "1f7r" [edit=sysop:move=sysop]

OCA — Wed, 14 Nov 2012 07:21:24 GMT

Protected "1f7r" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:21, 14 November 2012