1lj8 - Revision history

OCA at 08:09, 3 April 2024

2024-04-03T08:09:51Z

←Older revision		Revision as of 08:09, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='1lj8' size='340' side='right'caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lj8' size='340' side='right'caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</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]] 1.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1m2w\|1m2w]]~~</~~div></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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [https://pdbe.org/1lj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [https://www.ebi.ac.uk/pdbsum/1lj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lj8 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [~~http~~://pdbe.org/1lj8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lj8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lj8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O08355_PSEFL O08355_PSEFL]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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=1lj8 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=1lj8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Long-chain mannitol dehydrogenases are secondary alcohol dehydrogenases that are of wide interest because of their involvement in metabolism and potential applications in agriculture, medicine, and industry. They differ from other alcohol and polyol dehydrogenases because they do not contain a conserved tyrosine and are not dependent on Zn(2+) or other metal cofactors. The structures of the long-chain mannitol 2-dehydrogenase (54 kDa) from Pseudomonas fluorescens in a binary complex with NAD(+) and ternary complex with NAD(+) and d-mannitol have been determined to resolutions of 1.7 and 1.8 A and R-factors of 0.171 and 0.176, respectively. These results show an N-terminal domain that includes a typical Rossmann fold. The C-terminal domain is primarily alpha-helical and mediates mannitol binding. The electron lone pair of Lys-295 is steered by hydrogen-bonding interactions with the amide oxygen of Asn-300 and the main-chain carbonyl oxygen of Val-229 to act as the general base. Asn-191 and Asn-300 are involved in a web of hydrogen bonding, which precisely orients the mannitol O2 proton for abstraction. These residues also aid in stabilizing a negative charge in the intermediate state and in preventing the formation of nonproductive complexes with the substrate. The catalytic lysine may be returned to its unprotonated state using a rectifying proton tunnel driven by Glu-292 oscillating among different environments. Despite low sequence homology, the closest structural neighbors are glycerol-3-phosphate dehydrogenase, N-(1-d-carboxylethyl)-l-norvaline dehydrogenase, UDP-glucose dehydrogenase, and 6-phosphogluconate dehydrogenase, indicating a possible evolutionary relationship among these enzymes.
-
-	Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism.,Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK J Biol Chem. 2002 Nov 8;277(45):43433-42. Epub 2002 Aug 23. PMID:12196534<ref>PMID:12196534</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lj8" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mannitol 2-dehydrogenase~~]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Kavanagh~~, K L~~]]	+	[[Category: Kavanagh KL]]
-	[[Category: Klimacek, M]]	+	[[Category: Klimacek M]]
-	[[Category: Nidetzky, B]]	+	[[Category: Nidetzky B]]
-	[[Category: Wilson~~, D K]]~~	+	[[Category: Wilson DK]]
-	~~[[Category: Long-chain dehydrogenase]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:59, 25 November 2020

2020-11-25T07:59:06Z

OCA at 21:41, 24 January 2018

2018-01-24T21:41:59Z

←Older revision		Revision as of 21:41, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of mannitol dehydrogenase in complex with NAD==		==Crystal structure of mannitol dehydrogenase in complex with NAD==
	<StructureSection load='1lj8' size='340' side='right' caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lj8' size='340' side='right' caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://pdbe.org/1lj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://pdbe.org/1lj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lj8 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/1lj8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/1lj8_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 15:24, 8 February 2016

2016-02-08T15:24:06Z

←Older revision		Revision as of 15:24, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lj8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:55, 10 September 2015

2015-09-10T12:55:31Z

←Older revision		Revision as of 12:55, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1lj8' size='340' side='right' caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lj8' size='340' side='right' caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_fluorescens Pseudomonas~~ fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2w\|1m2w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2w\|1m2w]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 ~~Pseudomonas~~ fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://pdbe.org/1lj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1lj8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
-	[[Category: Pseudomonas fluorescens]]
	[[Category: Kavanagh, K L]]		[[Category: Kavanagh, K L]]
	[[Category: Klimacek, M]]		[[Category: Klimacek, M]]

OCA at 16:59, 5 January 2015

2015-01-05T16:59:08Z

←Older revision		Revision as of 16:59, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2w\|1m2w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2w\|1m2w]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 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 34:		Line 34:
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Kavanagh, K L.]]	+	[[Category: Kavanagh, K L]]
-	[[Category: Klimacek, M.]]	+	[[Category: Klimacek, M]]
-	[[Category: Nidetzky, B.]]	+	[[Category: Nidetzky, B]]
-	[[Category: Wilson, D K.]]	+	[[Category: Wilson, D K]]
	[[Category: Long-chain dehydrogenase]]		[[Category: Long-chain dehydrogenase]]
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 15:12, 28 September 2014

2014-09-28T15:12:07Z

←Older revision		Revision as of 15:12, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lj8.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of mannitol dehydrogenase in complex with NAD==
		+	<StructureSection load='1lj8' size='340' side='right' caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2w\|1m2w]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 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/lj/1lj8_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 ==
		+	Long-chain mannitol dehydrogenases are secondary alcohol dehydrogenases that are of wide interest because of their involvement in metabolism and potential applications in agriculture, medicine, and industry. They differ from other alcohol and polyol dehydrogenases because they do not contain a conserved tyrosine and are not dependent on Zn(2+) or other metal cofactors. The structures of the long-chain mannitol 2-dehydrogenase (54 kDa) from Pseudomonas fluorescens in a binary complex with NAD(+) and ternary complex with NAD(+) and d-mannitol have been determined to resolutions of 1.7 and 1.8 A and R-factors of 0.171 and 0.176, respectively. These results show an N-terminal domain that includes a typical Rossmann fold. The C-terminal domain is primarily alpha-helical and mediates mannitol binding. The electron lone pair of Lys-295 is steered by hydrogen-bonding interactions with the amide oxygen of Asn-300 and the main-chain carbonyl oxygen of Val-229 to act as the general base. Asn-191 and Asn-300 are involved in a web of hydrogen bonding, which precisely orients the mannitol O2 proton for abstraction. These residues also aid in stabilizing a negative charge in the intermediate state and in preventing the formation of nonproductive complexes with the substrate. The catalytic lysine may be returned to its unprotonated state using a rectifying proton tunnel driven by Glu-292 oscillating among different environments. Despite low sequence homology, the closest structural neighbors are glycerol-3-phosphate dehydrogenase, N-(1-d-carboxylethyl)-l-norvaline dehydrogenase, UDP-glucose dehydrogenase, and 6-phosphogluconate dehydrogenase, indicating a possible evolutionary relationship among these enzymes.

-	~~{{STRUCTURE_1lj8\| PDB=1lj8 \| SCENE= }}~~	+	Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism.,Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK J Biol Chem. 2002 Nov 8;277(45):43433-42. Epub 2002 Aug 23. PMID:12196534<ref>PMID:12196534</ref>

-	~~===Crystal structure~~ of ~~mannitol dehydrogenase in complex with NAD===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12196534}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1lj8]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012196534<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]

OCA: Protected "1lj8" [edit=sysop:move=sysop]

2012-12-05T21:16:42Z

Protected "1lj8" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:16, 5 December 2012

OCA at 21:16, 5 December 2012

2012-12-05T21:16:39Z

←Older revision		Revision as of 21:16, 5 December 2012
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-	{{Seed}}
	[[Image:1lj8.png\|left\|200px]]		[[Image:1lj8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lj8", 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_1lj8\| PDB=1lj8 \| SCENE= }}		{{STRUCTURE_1lj8\| PDB=1lj8 \| SCENE= }}

	===Crystal structure of mannitol dehydrogenase in complex with NAD===		===Crystal structure of mannitol dehydrogenase in complex with NAD===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12196534}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12196534 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12196534}}		{{ABSTRACT_PUBMED_12196534}}

	==About this Structure==		==About this Structure==
-	~~1LJ8~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA].	+	[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12196534~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012196534</ref><references group="xtra"/>
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
Line 33:		Line 21:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:59:49 2009''

OCA at 21:59, 16 February 2009

2009-02-16T21:59:50Z

←Older revision		Revision as of 21:59, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1LJ8 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA].	+	1LJ8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA].

	==Reference==		==Reference==
-	Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism., Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK, J Biol Chem. 2002 Nov 8;277(45):43433-42. Epub 2002 Aug 23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12196534 12196534]~~	+	<ref group="xtra">PMID:12196534</ref><references group="xtra"/>
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Single protein]]
	[[Category: Kavanagh, K L.]]		[[Category: Kavanagh, K L.]]
	[[Category: Klimacek, M.]]		[[Category: Klimacek, M.]]
Line 35:		Line 34:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 21~~:00:~~29 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:59:49 2009''

←Older revision		Revision as of 07:59, 25 November 2020
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	==Crystal structure of mannitol dehydrogenase in complex with NAD==		==Crystal structure of mannitol dehydrogenase in complex with NAD==
-	<StructureSection load='1lj8' size='340' side='right' caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1lj8' size='340' side='right'caption='[[1lj8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LJ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m2w\|1m2w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m2w\|1m2w]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://pdbe.org/1lj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lj8 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=1lj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lj8 OCA], [http://pdbe.org/1lj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lj8 RCSB], [http://www.ebi.ac.uk/pdbsum/1lj8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lj8 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Kavanagh, K L]]		[[Category: Kavanagh, K L]]