2qjo - Revision history

OCA at 09:16, 21 February 2024

OCA — Wed, 21 Feb 2024 09:16:35 GMT

←Older revision		Revision as of 09:16, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2qjo' size='340' side='right'caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2qjo' size='340' side='right'caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aphanocapsa_sp~~.~~_(strain_n-1) Aphanocapsa~~ sp. ~~(strain n-1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.6Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [https://pdbe.org/2qjo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [https://www.ebi.ac.uk/pdbsum/2qjo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjo 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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [https://pdbe.org/2qjo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [https://www.ebi.ac.uk/pdbsum/2qjo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NADM_SYNY3 NADM_SYNY3]] The Nudix hydrolase domain is active on ADP-ribose, (2')-phospho-ADP-ribose, IDP-ribose and NADPH.	+	[https://www.uniprot.org/uniprot/NADM_SYNY3 NADM_SYNY3] The Nudix hydrolase domain is active on ADP-ribose, (2')-phospho-ADP-ribose, IDP-ribose and NADPH.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=2qjo 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=2qjo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2.
-
-	Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism.,Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H Structure. 2008 Feb;16(2):196-209. PMID:18275811<ref>PMID:18275811</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2qjo" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brautigan, C]]	+	[[Category: Synechocystis sp. PCC 6803]]
-	[[Category: Grishin~~, N V~~]]	+	[[Category: Brautigan C]]
-	[[Category: Huang, N]]	+	[[Category: Grishin NV]]
-	[[Category: Magni, G]]	+	[[Category: Huang N]]
-	[[Category: Osterman, A]]	+	[[Category: Magni G]]
-	[[Category: Raffaelli, N]]	+	[[Category: Osterman A]]
-	[[Category: Sorci, L]]	+	[[Category: Raffaelli N]]
-	[[Category: Zhang, H]]	+	[[Category: Sorci L]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang H]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Zhang X]]
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Two individual domain~~]]	+

OCA at 08:22, 25 June 2021

OCA — Fri, 25 Jun 2021 08:22:08 GMT

←Older revision		Revision as of 08:22, 25 June 2021
Line 1:		Line 1:

	==crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.==		==crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.==
-	<StructureSection load='2qjo' size='340' side='right' caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='2qjo' size='340' side='right'caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [~~http~~://pdbe.org/2qjo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qjo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjo 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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [https://pdbe.org/2qjo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [https://www.ebi.ac.uk/pdbsum/2qjo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NADM_SYNY3 NADM_SYNY3]] The Nudix hydrolase domain is active on ADP-ribose, (2')-phospho-ADP-ribose, IDP-ribose and NADPH.	+	[[https://www.uniprot.org/uniprot/NADM_SYNY3 NADM_SYNY3]] The Nudix hydrolase domain is active on ADP-ribose, (2')-phospho-ADP-ribose, IDP-ribose and NADPH.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/2qjo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/2qjo_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 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brautigan, C]]		[[Category: Brautigan, C]]
	[[Category: Grishin, N V]]		[[Category: Grishin, N V]]

OCA at 09:50, 18 October 2017

OCA — Wed, 18 Oct 2017 09:50:06 GMT

←Older revision		Revision as of 09:50, 18 October 2017
Line 1:		Line 1:
		+
	==crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.==		==crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.==
	<StructureSection load='2qjo' size='340' side='right' caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2qjo' size='340' side='right' caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://pdbe.org/2qjo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo 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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://pdbe.org/2qjo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qjo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:15, 11 September 2015

OCA — Fri, 11 Sep 2015 13:15:58 GMT

←Older revision		Revision as of 13:15, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2qjo' size='340' side='right' caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2qjo' size='340' side='right' caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Synechocystis_sp~~. ~~Synechocystis~~ sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1143 Synechocystis~~ sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo 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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://pdbe.org/2qjo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		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 2qjo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Synechocystis sp]]
	[[Category: Brautigan, C]]		[[Category: Brautigan, C]]
	[[Category: Grishin, N V]]		[[Category: Grishin, N V]]

OCA at 16:56, 25 December 2014

OCA — Thu, 25 Dec 2014 16:56:10 GMT

←Older revision		Revision as of 16:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1143 Synechocystis sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1143 Synechocystis sp.])</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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo 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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NADM_SYNY3 NADM_SYNY3]] The Nudix hydrolase domain is active on ADP-ribose, (2')-phospho-ADP-ribose, IDP-ribose and NADPH.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Synechocystis sp.]]	+	[[Category: Synechocystis sp]]
-	[[Category: Brautigan, C.]]	+	[[Category: Brautigan, C]]
-	[[Category: Grishin, N V.]]	+	[[Category: Grishin, N V]]
-	[[Category: Huang, N.]]	+	[[Category: Huang, N]]
-	[[Category: Magni, G.]]	+	[[Category: Magni, G]]
-	[[Category: Osterman, A.]]	+	[[Category: Osterman, A]]
-	[[Category: Raffaelli, N.]]	+	[[Category: Raffaelli, N]]
-	[[Category: Sorci, L.]]	+	[[Category: Sorci, L]]
-	[[Category: Zhang, H.]]	+	[[Category: Zhang, H]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Two individual domain]]		[[Category: Two individual domain]]

OCA at 20:14, 30 September 2014

OCA — Tue, 30 Sep 2014 20:14:53 GMT

←Older revision		Revision as of 20:14, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qjo.~~png~~\|~~left~~\|200px]]	+	==crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.==
		+	<StructureSection load='2qjo' size='340' side='right' caption='[[2qjo]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qjo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">slr0787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1143 Synechocystis sp.])</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=2qjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjo RCSB], [http://www.ebi.ac.uk/pdbsum/2qjo 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/qj/2qjo_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 ==
		+	Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2.

-	~~{{STRUCTURE_2qjo\| PDB=2qjo \| SCENE= }}~~	+	Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism.,Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H Structure. 2008 Feb;16(2):196-209. PMID:18275811<ref>PMID:18275811</ref>

-	~~===crystal structure of a bifunctional NMN adenylyltransferase~~/~~ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18275811}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2qjo]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Synechocystis_sp~~. ~~Synechocystis sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018275811<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Synechocystis sp.]]		[[Category: Synechocystis sp.]]
	[[Category: Brautigan, C.]]		[[Category: Brautigan, C.]]

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

OCA — Mon, 07 Jan 2013 20:23:29 GMT

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

←Older revision

Revision as of 20:23, 7 January 2013

OCA at 20:23, 7 January 2013

OCA — Mon, 07 Jan 2013 20:23:27 GMT

←Older revision		Revision as of 20:23, 7 January 2013
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-	{{Seed}}
	[[Image:2qjo.png\|left\|200px]]		[[Image:2qjo.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qjo", 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_2qjo\| PDB=2qjo \| SCENE= }}		{{STRUCTURE_2qjo\| PDB=2qjo \| SCENE= }}

	===crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.===		===crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18275811}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18275811 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18275811}}		{{ABSTRACT_PUBMED_18275811}}

	==About this Structure==		==About this Structure==
-	~~2QJO~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA].	+	[[2qjo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18275811~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018275811</ref><references group="xtra"/>
	[[Category: Synechocystis sp.]]		[[Category: Synechocystis sp.]]
	[[Category: Brautigan, C.]]		[[Category: Brautigan, C.]]
Line 37:		Line 25:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Two individual domain]]		[[Category: Two individual domain]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:27:29 2009''

OCA at 20:27, 17 February 2009

OCA — Tue, 17 Feb 2009 20:27:30 GMT

←Older revision		Revision as of 20:27, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2QJO is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA].	+	2QJO is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJO OCA].

	==Reference==		==Reference==
-	Bifunctional NMN Adenylyltransferase/ADP-Ribose Pyrophosphatase: Structure and Function in Bacterial NAD Metabolism., Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H, Structure. 2008 Feb;16(2):196-209. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18275811 18275811]~~	+	<ref group="xtra">PMID:18275811</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Synechocystis sp.]]		[[Category: Synechocystis sp.]]
	[[Category: Brautigan, C.]]		[[Category: Brautigan, C.]]
Line 39:		Line 38:
	[[Category: Two individual domain]]		[[Category: Two individual domain]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:40:~~18 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:27:29 2009''

OCA at 03:40, 29 July 2008

OCA — Tue, 29 Jul 2008 03:40:21 GMT

←Older revision		Revision as of 03:40, 29 July 2008
Line 1:		Line 1:
-	[[Image:2qjo.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2qjo.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2qjo\| PDB=2qjo \| SCENE= }}		{{STRUCTURE_2qjo\| PDB=2qjo \| SCENE= }}

-	~~'''~~crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.~~'''~~	+	===crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.===


-	~~==Overview==~~	+	<!--
-	~~Bacterial NadM~~-~~Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP~~-~~ribose (ADPR) pyrophosphatase domain. While most members of~~ this ~~enzyme family~~, ~~such as that from a model cyanobacterium Synechocystis sp.~~, ~~are involved primarily in nicotinamide adenine dinucleotide~~ (~~NAD) salvage~~/~~recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis~~. ~~The crystal structures of NadM-Nudix from both species~~, ~~including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of~~ the ~~substrate binding and catalytic sites in both domains~~. ~~The structure of the N~~-~~terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C~~-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca(2+) channel TRPM2.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18275811}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18275811 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18275811}}

	==About this Structure==		==About this Structure==
Line 34:		Line 38:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Two individual domain]]		[[Category: Two individual domain]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 15~~:04:22 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:40:18 2008''