1q27 - Revision history

OCA at 09:00, 22 May 2024

OCA — Wed, 22 May 2024 09:00:56 GMT

←Older revision		Revision as of 09:00, 22 May 2024
Line 19:		Line 19:
	</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=1q27 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=1q27 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight beta-strands and three alpha-helices organized into three subdomains: an N-terminal beta-sheet (1-34), a central Nudix core (35-140), and a C-terminal helix-turn-helix (141-171). The Nudix core and the C-terminal helix-turn-helix form the fundamental fold common to the Nudix family, a large mixed beta-sheet sandwiched between alpha-helices. The residues that compose the signature Nudix sequence, GX5EX7REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn-helix-turn motif on the face of the mixed beta-sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg2+. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl-diphosphate delta-isomerase and that it does not bind alpha,beta-methyleneadenosine 5'-triphosphate (AMPCPP) or guanosine 5'-[beta,gamma-imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed.
		+
		+	Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium.,Buchko GW, Ni S, Holbrook SR, Kennedy MA Proteins. 2004 Jul 1;56(1):28-39. PMID:15162484<ref>PMID:15162484</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1q27" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:00, 17 April 2024

OCA — Wed, 17 Apr 2024 06:00:46 GMT

←Older revision		Revision as of 06:00, 17 April 2024
Line 1:		Line 1:

	==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==		==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==
-	<StructureSection load='1q27' size='340' side='right'caption='[[1q27~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='1q27' size='340' side='right'caption='[[1q27]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus~~ radiodurans~~" raj et al. 1960~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DR0079 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1299~~ "~~Micrococcus radiodurans~~" ~~Raj et al. 1960])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [https://pdbe.org/1q27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [https://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [https://pdbe.org/1q27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [https://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA]] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</ref>	+	[https://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</ref>
	== 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=1q27 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=1q27 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight beta-strands and three alpha-helices organized into three subdomains: an N-terminal beta-sheet (1-34), a central Nudix core (35-140), and a C-terminal helix-turn-helix (141-171). The Nudix core and the C-terminal helix-turn-helix form the fundamental fold common to the Nudix family, a large mixed beta-sheet sandwiched between alpha-helices. The residues that compose the signature Nudix sequence, GX5EX7REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn-helix-turn motif on the face of the mixed beta-sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg2+. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl-diphosphate delta-isomerase and that it does not bind alpha,beta-methyleneadenosine 5'-triphosphate (AMPCPP) or guanosine 5'-[beta,gamma-imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed.
-
-	Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium.,Buchko GW, Ni S, Holbrook SR, Kennedy MA Proteins. 2004 Jul 1;56(1):28-39. PMID:15162484<ref>PMID:15162484</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1q27" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Micrococcus~~ radiodurans ~~raj et al. 1960~~]]	+	[[Category: Deinococcus radiodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Buchko~~, G W~~]]	+	[[Category: Buchko GW]]
-	[[Category: Holbrook~~, S R~~]]	+	[[Category: Holbrook SR]]
-	[[Category: Kennedy~~, M A~~]]	+	[[Category: Kennedy MA]]
-	[[Category: Ni, S]]	+	[[Category: Ni S]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nudix hydrolase]]~~	+
-	~~[[Category: Radiation resistance~~]]	+

OCA at 06:25, 2 March 2022

OCA — Wed, 02 Mar 2022 06:25:58 GMT

←Older revision		Revision as of 06:25, 2 March 2022
Line 3:		Line 3:
	<StructureSection load='1q27' size='340' side='right'caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1q27' size='340' side='right'caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [~~http~~://pdbe.org/1q27 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [https://pdbe.org/1q27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [https://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA]] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</ref>	+	[[https://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA]] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:41, 9 December 2020

OCA — Wed, 09 Dec 2020 07:41:41 GMT

←Older revision		Revision as of 07:41, 9 December 2020
Line 1:		Line 1:

	==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==		==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==
-	<StructureSection load='1q27' size='340' side='right' caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='1q27' size='340' side='right'caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://pdbe.org/1q27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://pdbe.org/1q27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Micrococcus radiodurans raj et al. 1960]]		[[Category: Micrococcus radiodurans raj et al. 1960]]
		+	[[Category: Large Structures]]
	[[Category: Buchko, G W]]		[[Category: Buchko, G W]]
	[[Category: Holbrook, S R]]		[[Category: Holbrook, S R]]

OCA at 08:15, 24 February 2018

OCA — Sat, 24 Feb 2018 08:15:13 GMT

←Older revision		Revision as of 08:15, 24 February 2018
Line 1:		Line 1:
		+
	==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==		==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==
	<StructureSection load='1q27' size='340' side='right' caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1q27' size='340' side='right' caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://pdbe.org/1q27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://pdbe.org/1q27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q27 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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/q2/1q27_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/1q27_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 11:17, 7 February 2016

OCA — Sun, 07 Feb 2016 11:17:17 GMT

←Older revision		Revision as of 11:17, 7 February 2016
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=1q27 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:58, 10 September 2015

OCA — Thu, 10 Sep 2015 00:58:48 GMT

←Older revision		Revision as of 00:58, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1q27' size='340' side='right' caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1q27' size='340' side='right' caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Deinococcus_radiodurans Deinococcus~~ radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 ~~Deinococcus~~ radiodurans])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://pdbe.org/1q27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1q27" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deinococcus~~ radiodurans]]	+	[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Buchko, G W]]		[[Category: Buchko, G W]]
	[[Category: Holbrook, S R]]		[[Category: Holbrook, S R]]

OCA at 14:41, 24 December 2014

OCA — Wed, 24 Dec 2014 14:41:13 GMT

←Older revision		Revision as of 14:41, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Y079_DEIRA Y079_DEIRA]] Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.<ref>PMID:15162484</ref> <ref>PMID:18512963</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
-	[[Category: Buchko, G W.]]	+	[[Category: Buchko, G W]]
-	[[Category: Holbrook, S R.]]	+	[[Category: Holbrook, S R]]
-	[[Category: Kennedy, M A.]]	+	[[Category: Kennedy, M A]]
-	[[Category: Ni, S.]]	+	[[Category: Ni, S]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nudix hydrolase]]		[[Category: Nudix hydrolase]]
	[[Category: Radiation resistance]]		[[Category: Radiation resistance]]

OCA at 16:04, 29 September 2014

OCA — Mon, 29 Sep 2014 16:04:58 GMT

←Older revision		Revision as of 16:04, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1q27.~~png\|left~~\|200px]]	+	==NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans==
		+	<StructureSection load='1q27' size='340' side='right' caption='[[1q27]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q27]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q27 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR0079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</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=1q27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q27 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q27 RCSB], [http://www.ebi.ac.uk/pdbsum/1q27 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/q2/1q27_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 ==
		+	Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight beta-strands and three alpha-helices organized into three subdomains: an N-terminal beta-sheet (1-34), a central Nudix core (35-140), and a C-terminal helix-turn-helix (141-171). The Nudix core and the C-terminal helix-turn-helix form the fundamental fold common to the Nudix family, a large mixed beta-sheet sandwiched between alpha-helices. The residues that compose the signature Nudix sequence, GX5EX7REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn-helix-turn motif on the face of the mixed beta-sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg2+. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl-diphosphate delta-isomerase and that it does not bind alpha,beta-methyleneadenosine 5'-triphosphate (AMPCPP) or guanosine 5'-[beta,gamma-imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed.

-	~~{{STRUCTURE_1q27\| PDB=1q27 \| SCENE= }}~~	+	Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium.,Buchko GW, Ni S, Holbrook SR, Kennedy MA Proteins. 2004 Jul 1;56(1):28-39. PMID:15162484<ref>PMID:15162484</ref>

-	~~===NMR Solution Structure~~ of ~~DR0079: An hypothetical Nudix protein from D~~. ~~radiodurans===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15162484}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1q27]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q27 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015162484<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Buchko, G W.]]		[[Category: Buchko, G W.]]

OCA: Protected "1q27" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 09:48:25 GMT

Protected "1q27" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:48, 2 January 2013