2vkq - Revision history

OCA at 15:23, 13 December 2023

2023-12-13T15:23:24Z

←Older revision		Revision as of 15:23, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2vkq' size='340' side='right'caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2vkq' size='340' side='right'caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2jga\|2jga]], [[2cn1\|2cn1]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5]~~ </~~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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [https://pdbe.org/2vkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [https://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq 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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [https://pdbe.org/2vkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [https://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/5NT3A_HUMAN 5NT3A_HUMAN] Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency. The disease is caused by variants affecting the gene represented in this entry.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/5NT3A_HUMAN 5NT3A_HUMAN] Nucleotidase which shows specific activity towards cytidine monophosphate (CMP) and 7-methylguanosine monophosphate (m(7)GMP) (PubMed:24603684). CMP seems to be the preferred substrate (PubMed:15968458).<ref>PMID:15968458</ref> <ref>PMID:24603684</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 22:
	</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=2vkq 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=2vkq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the cell. It possesses phosphotransferase activity and thereby also catalyzes the reverse reaction. Both reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic 5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The tetrameric enzyme is structurally similar to enzymes of the haloacid dehalogenase (HAD) superfamily, including mitochondrial 5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses additional regulatory regions that contain two allosteric effector sites. At effector site 1 located near a subunit interface we modeled diadenosine tetraphosphate with one adenosine moiety in each subunit. This efficiently glues the tetramer subunits together in pairs. The model shows why diadenosine tetraphosphate but not diadenosine triphosphate activates the enzyme and supports a role for cN-II during apoptosis when the level of diadenosine tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in effector site 1 using one phosphate site from each subunit. By comparing the structure of cytosolic 5'-nucleotidase II with that of mitochondrial 5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues involved in substrate recognition.
-
-	Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition.,Wallden K, Stenmark P, Nyman T, Flodin S, Graslund S, Loppnau P, Bianchi V, Nordlund P J Biol Chem. 2007 Jun 15;282(24):17828-36. Epub 2007 Apr 3. PMID:17405878<ref>PMID:17405878</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2vkq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~5'-nucleotidase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H]]~~	+	[[Category: Arrowsmith CH]]
-	~~[[Category: Berg, S van den~~]]	+	[[Category: Berglund H]]
-	[[Category: Berglund, H]]	+	[[Category: Busam R]]
-	[[Category: Busam, R]]	+	[[Category: Collins R]]
-	[[Category: Collins, R]]	+	[[Category: Dahlgren LG]]
-	[[Category: Dahlgren~~, L G~~]]	+	[[Category: Edwards A]]
-	[[Category: Edwards, A]]	+	[[Category: Flodin S]]
-	[[Category: Flodin, S]]	+	[[Category: Flores A]]
-	[[Category: Flores, A]]	+	[[Category: Graslund S]]
-	[[Category: Graslund, S]]	+	[[Category: Hammarstrom M]]
-	[[Category: Hammarstrom, M]]	+	[[Category: Herman MD]]
-	[[Category: Herman~~, M D~~]]	+	[[Category: Johansson A]]
-	[[Category: Johansson, A]]	+	[[Category: Johansson I]]
-	[[Category: Johansson, I]]	+	[[Category: Kallas A]]
-	[[Category: Kallas, A]]	+	[[Category: Karlberg T]]
-	[[Category: Karlberg, T]]	+	[[Category: Kotenyova T]]
-	[[Category: Kotenyova, T]]	+	[[Category: Lehtio L]]
-	[[Category: Lehtio, L]]	+	[[Category: Moche M]]
-	[[Category: Moche, M]]	+	[[Category: Nilsson ME]]
-	[[Category: Nilsson~~, M E~~]]	+	[[Category: Nordlund P]]
-	[[Category: Nordlund, P]]	+	[[Category: Nyman T]]
-	[[Category: Nyman, T]]	+	[[Category: Persson C]]
-	[[Category: Persson, C]]	+	[[Category: Sagemark J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Thorsell AG]]
-	[[Category: Sagemark, J]]	+	[[Category: Tresaugues L]]
-	[[Category: Thorsell~~, A G~~]]	+	[[Category: Wallden K]]
-	[[Category: Tresaugues, L]]	+	[[Category: Weigelt J]]
-	[[Category: Wallden, K]]	+	[[Category: Welin M]]
-	[[Category: Weigelt, J]]	+	[[Category: Van den Berg S]]
-	[[Category: Welin, M]]	+
-	[[Category: ~~Disease mutation]]~~	+
-	~~[[Category: Endoplasmic reticulum]]~~	+
-	~~[[Category: Hemolytic anemia]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotidase]]~~	+
-	~~[[Category: Nucleotide metabolism]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Phosphotransferase~~]]	+

OCA at 11:39, 30 March 2022

2022-03-30T11:39:09Z

←Older revision		Revision as of 11:39, 30 March 2022
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	<StructureSection load='2vkq' size='340' side='right'caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2vkq' size='340' side='right'caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jga\|2jga]], [[2cn1\|2cn1]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [~~http~~://pdbe.org/2vkq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq 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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [https://pdbe.org/2vkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [https://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:04, 25 June 2020

2020-06-25T08:04:25Z

←Older revision		Revision as of 08:04, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride==		==Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride==
-	<StructureSection load='2vkq' size='340' side='right' caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2vkq' size='340' side='right'caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://pdbe.org/2vkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq 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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://pdbe.org/2vkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	[[Category: 5'-nucleotidase]]		[[Category: 5'-nucleotidase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Berg, S van den]]		[[Category: Berg, S van den]]

OCA at 20:38, 19 September 2018

2018-09-19T20:38:55Z

←Older revision		Revision as of 20:38, 19 September 2018
Line 1:		Line 1:
		+
	==Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride==		==Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride==
	<StructureSection load='2vkq' size='340' side='right' caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2vkq' size='340' side='right' caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://pdbe.org/2vkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq 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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://pdbe.org/2vkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vkq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vkq_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 04:18, 10 February 2016

2016-02-10T04:18:41Z

←Older revision		Revision as of 04:18, 10 February 2016
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq 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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://pdbe.org/2vkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=2vkq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 2vkq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:48, 22 April 2015

2015-04-22T06:48:23Z

←Older revision		Revision as of 06:48, 22 April 2015
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC~~ 5'-~~NUCLEOTIDASE~~ III (CN-III, NT5C3) ~~IN COMPLEX WITH BERYLLIUM TRIFLUORIDE~~==	+	==Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride==
	<StructureSection load='2vkq' size='340' side='right' caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2vkq' size='340' side='right' caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: 5'-nucleotidase]]		[[Category: 5'-nucleotidase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
-	[[Category: Berg, S ~~Van Den~~]]	+	[[Category: Berg, S van den]]
	[[Category: Berglund, H]]		[[Category: Berglund, H]]
	[[Category: Busam, R]]		[[Category: Busam, R]]
Line 55:		Line 55:
	[[Category: Nyman, T]]		[[Category: Nyman, T]]
	[[Category: Persson, C]]		[[Category: Persson, C]]
-	[[Category: Sagemark, J]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Sagemark, J]]
	[[Category: Thorsell, A G]]		[[Category: Thorsell, A G]]
	[[Category: Tresaugues, L]]		[[Category: Tresaugues, L]]

OCA at 15:01, 19 January 2015

2015-01-19T15:01:55Z

←Older revision		Revision as of 15:01, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq 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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq 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: 5'-nucleotidase]]		[[Category: 5'-nucleotidase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Berg, S Van Den.]]	+	[[Category: Berg, S Van Den]]
-	[[Category: Berglund, H.]]	+	[[Category: Berglund, H]]
-	[[Category: Busam, R.]]	+	[[Category: Busam, R]]
-	[[Category: Collins, R.]]	+	[[Category: Collins, R]]
-	[[Category: Dahlgren, L G.]]	+	[[Category: Dahlgren, L G]]
-	[[Category: Edwards, A.]]	+	[[Category: Edwards, A]]
-	[[Category: Flodin, S.]]	+	[[Category: Flodin, S]]
-	[[Category: Flores, A.]]	+	[[Category: Flores, A]]
-	[[Category: Graslund, S.]]	+	[[Category: Graslund, S]]
-	[[Category: Hammarstrom, M.]]	+	[[Category: Hammarstrom, M]]
-	[[Category: Herman, M D.]]	+	[[Category: Herman, M D]]
-	[[Category: Johansson, A.]]	+	[[Category: Johansson, A]]
-	[[Category: Johansson, I.]]	+	[[Category: Johansson, I]]
-	[[Category: Kallas, A.]]	+	[[Category: Kallas, A]]
-	[[Category: Karlberg, T.]]	+	[[Category: Karlberg, T]]
-	[[Category: Kotenyova, T.]]	+	[[Category: Kotenyova, T]]
-	[[Category: Lehtio, L.]]	+	[[Category: Lehtio, L]]
-	[[Category: Moche, M.]]	+	[[Category: Moche, M]]
-	[[Category: Nilsson, M E.]]	+	[[Category: Nilsson, M E]]
-	[[Category: Nordlund, P.]]	+	[[Category: Nordlund, P]]
-	[[Category: Nyman, T.]]	+	[[Category: Nyman, T]]
-	[[Category: Persson, C.]]	+	[[Category: Persson, C]]
-	[[Category: Sagemark, J.]]	+	[[Category: Sagemark, J]]
-	[[Category: ~~Sgc,~~ Structural ~~GenomicsConsortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Thorsell, A G.]]	+	[[Category: Thorsell, A G]]
-	[[Category: Tresaugues, L.]]	+	[[Category: Tresaugues, L]]
-	[[Category: Wallden, K.]]	+	[[Category: Wallden, K]]
-	[[Category: Weigelt, J.]]	+	[[Category: Weigelt, J]]
-	[[Category: Welin, M.]]	+	[[Category: Welin, M]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]
	[[Category: Endoplasmic reticulum]]		[[Category: Endoplasmic reticulum]]

OCA at 01:52, 1 October 2014

2014-10-01T01:52:20Z

←Older revision		Revision as of 01:52, 1 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2vkq\| PDB=2vkq \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III (CN-III, NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE==
-	===CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III (CN-III, NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE===	+	<StructureSection load='2vkq' size='340' side='right' caption='[[2vkq]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17405878}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jga\|2jga]], [[2cn1\|2cn1]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [http://www.ebi.ac.uk/pdbsum/2vkq 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/vk/2vkq_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 ==
		+	Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the cell. It possesses phosphotransferase activity and thereby also catalyzes the reverse reaction. Both reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic 5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The tetrameric enzyme is structurally similar to enzymes of the haloacid dehalogenase (HAD) superfamily, including mitochondrial 5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses additional regulatory regions that contain two allosteric effector sites. At effector site 1 located near a subunit interface we modeled diadenosine tetraphosphate with one adenosine moiety in each subunit. This efficiently glues the tetramer subunits together in pairs. The model shows why diadenosine tetraphosphate but not diadenosine triphosphate activates the enzyme and supports a role for cN-II during apoptosis when the level of diadenosine tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in effector site 1 using one phosphate site from each subunit. By comparing the structure of cytosolic 5'-nucleotidase II with that of mitochondrial 5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues involved in substrate recognition.

-	~~==About this Structure==~~	+	Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition.,Wallden K, Stenmark P, Nyman T, Flodin S, Graslund S, Loppnau P, Bianchi V, Nordlund P J Biol Chem. 2007 Jun 15;282(24):17828-36. Epub 2007 Apr 3. PMID:17405878<ref>PMID:17405878</ref>
-	~~[[2vkq]] is a 1 chain~~ structure ~~with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2VKQ OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:017405878</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: 5'-nucleotidase]]		[[Category: 5'-nucleotidase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 23:58, 24 March 2013

2013-03-24T23:58:17Z

←Older revision		Revision as of 23:58, 24 March 2013
Line 1:		Line 1:
-	[[Image:2vkq.png\|left\|200px]]
-
	{{STRUCTURE_2vkq\| PDB=2vkq \| SCENE= }}		{{STRUCTURE_2vkq\| PDB=2vkq \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III (CN-III, NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE===		===CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III (CN-III, NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE===
-
	{{ABSTRACT_PUBMED_17405878}}		{{ABSTRACT_PUBMED_17405878}}

Line 11:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:017405878</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017405878</ref><references group="xtra"/><references/>
	[[Category: 5'-nucleotidase]]		[[Category: 5'-nucleotidase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA: Protected "2vkq" [edit=sysop:move=sysop]

2013-01-07T18:33:33Z

Protected "2vkq" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:33, 7 January 2013