1xjf - Revision history

OCA at 06:46, 23 August 2023

OCA — Wed, 23 Aug 2023 06:46:24 GMT

←Older revision		Revision as of 06:46, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1xjf' size='340' side='right'caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1xjf' size='340' side='right'caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XJF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DTP:2~~-~~DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~2336 ATCC 43589])</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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [https://pdbe.org/1xjf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [https://www.ebi.ac.uk/pdbsum/1xjf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjf ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [~~http~~://pdbe.org/1xjf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xjf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O33839_THEMT O33839_THEMT]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ribonucleoside-diphosphate reductase~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: Eliasson, R]]	+	[[Category: Eliasson R]]
-	[[Category: Jordan, A]]	+	[[Category: Jordan A]]
-	[[Category: Larsson, K M]]	+	[[Category: Larsson K-M]]
-	[[Category: Logan~~, D T~~]]	+	[[Category: Logan DT]]
-	[[Category: Nordlund, P]]	+	[[Category: Nordlund P]]
-	[[Category: Reichard, P]]	+	[[Category: Reichard P]]
-	~~[[Category: 10 alpha-beta barrel]]~~	+
-	~~[[Category: Allosteric regulation]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein-nucleotide complex]]~~	+
-	~~[[Category: Ribonucleotide reductase]]~~	+
-	~~[[Category: Substrate specificity~~]]	+

OCA at 10:02, 6 January 2021

OCA — Wed, 06 Jan 2021 10:02:13 GMT

←Older revision		Revision as of 10:02, 6 January 2021
Line 1:		Line 1:

	==Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex==		==Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex==
-	<StructureSection load='1xjf' size='340' side='right' caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1xjf' size='340' side='right'caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XJF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://pdbe.org/1xjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjf ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://pdbe.org/1xjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xj/1xjf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xj/1xjf_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>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1xjf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xjf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43589]]		[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Eliasson, R]]		[[Category: Eliasson, R]]

OCA at 10:34, 12 October 2017

OCA — Thu, 12 Oct 2017 10:34:07 GMT

←Older revision		Revision as of 10:34, 12 October 2017
Line 1:		Line 1:
		+
	==Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex==		==Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex==
	<StructureSection load='1xjf' size='340' side='right' caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1xjf' size='340' side='right' caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://pdbe.org/1xjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf 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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://pdbe.org/1xjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1xjf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xjf" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:43, 9 February 2016

OCA — Tue, 09 Feb 2016 00:43:16 GMT

←Older revision		Revision as of 00:43, 9 February 2016
Line 17:		Line 17:
	<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=1xjf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:56, 10 September 2015

OCA — Thu, 10 Sep 2015 16:56:27 GMT

←Older revision		Revision as of 16:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xjf' size='340' side='right' caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1xjf' size='340' side='right' caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermotoga_maritima Thermotoga maritima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XJF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ~~Thermotoga maritima~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf 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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://pdbe.org/1xjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf PDBsum]</span></td></tr>
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/O33839_THEMA O33839_THEMA]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[RuleBase:RU003410]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 27:
	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 1xjf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43589]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
-	[[Category: Thermotoga maritima]]
	[[Category: Eliasson, R]]		[[Category: Eliasson, R]]
	[[Category: Jordan, A]]		[[Category: Jordan, A]]

OCA at 03:16, 25 December 2014

OCA — Thu, 25 Dec 2014 03:16:40 GMT

←Older revision		Revision as of 03:16, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XJF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XJF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf 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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/O33839_THEMA O33839_THEMA]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[RuleBase:RU003410]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-	[[Category: Eliasson, R.]]	+	[[Category: Eliasson, R]]
-	[[Category: Jordan, A.]]	+	[[Category: Jordan, A]]
-	[[Category: Larsson, K M.]]	+	[[Category: Larsson, K M]]
-	[[Category: Logan, D T.]]	+	[[Category: Logan, D T]]
-	[[Category: Nordlund, P.]]	+	[[Category: Nordlund, P]]
-	[[Category: Reichard, P.]]	+	[[Category: Reichard, P]]
	[[Category: 10 alpha-beta barrel]]		[[Category: 10 alpha-beta barrel]]
	[[Category: Allosteric regulation]]		[[Category: Allosteric regulation]]

OCA at 20:10, 28 September 2014

OCA — Sun, 28 Sep 2014 20:10:13 GMT

←Older revision		Revision as of 20:10, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xjf.~~png~~\|~~left~~\|200px]]	+	==Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex==
		+	<StructureSection load='1xjf' size='340' side='right' caption='[[1xjf]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XJF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xje\|1xje]], [[1xjg\|1xjg]], [[1xjj\|1xjj]], [[1xjk\|1xjk]], [[1xjm\|1xjm]], [[1xjn\|1xjn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdj ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [http://www.ebi.ac.uk/pdbsum/1xjf 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/xj/1xjf_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 ==
		+	Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.

-	~~{{STRUCTURE_1xjf\| PDB=1xjf \| SCENE= }}~~	+	Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.,Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P Nat Struct Mol Biol. 2004 Nov;11(11):1142-9. Epub 2004 Oct 10. PMID:15475969<ref>PMID:15475969</ref>

-	~~===Structural mechanism~~ of ~~allosteric substrate specificity in a ribonucleotide reductase: dATP complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15475969}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1xjf]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermotoga_maritima Thermotoga maritima]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]		*[[Ribonucleotide reductase\|Ribonucleotide reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015475969<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]

OCA at 12:02, 20 October 2012

OCA — Sat, 20 Oct 2012 12:02:29 GMT

←Older revision		Revision as of 12:02, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1xjf]] is a 2 chain structure ~~of [[Ribonucleotide reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA].	+	[[1xjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA].

	==See Also==		==See Also==

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

OCA — Thu, 26 Jul 2012 07:25:29 GMT

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

←Older revision

Revision as of 07:25, 26 July 2012

OCA at 07:25, 26 July 2012

OCA — Thu, 26 Jul 2012 07:25:27 GMT

←Older revision		Revision as of 07:25, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xjf.png\|left\|200px]]		[[Image:1xjf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xjf", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1xjf\| PDB=1xjf \| SCENE= }}		{{STRUCTURE_1xjf\| PDB=1xjf \| SCENE= }}

	===Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex===		===Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15475969}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15475969 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15475969}}		{{ABSTRACT_PUBMED_15475969}}

	==About this Structure==		==About this Structure==
-	~~1XJF~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA].	+	[[1xjf]] is a 2 chain structure of [[Ribonucleotide reductase]] with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA].
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15475969~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015475969</ref><references group="xtra"/>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
Line 34:		Line 25:
	[[Category: 10 alpha-beta barrel]]		[[Category: 10 alpha-beta barrel]]
	[[Category: Allosteric regulation]]		[[Category: Allosteric regulation]]
		+	[[Category: Oxidoreductase]]
	[[Category: Protein-nucleotide complex]]		[[Category: Protein-nucleotide complex]]
	[[Category: Ribonucleotide reductase]]		[[Category: Ribonucleotide reductase]]
	[[Category: Substrate specificity]]		[[Category: Substrate specificity]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:58:37 2009''