1n2s - Revision history

OCA at 07:51, 14 February 2024

OCA — Wed, 14 Feb 2024 07:51:47 GMT

←Older revision		Revision as of 07:51, 14 February 2024
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	<StructureSection load='1n2s' size='340' side='right'caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1n2s' size='340' side='right'caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1N2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N2S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4~~-~~DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>~~, ~~<scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~90371~~ "~~Bacillus typhimurium~~" ~~Loeffler 1892])~~<~~/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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [https://pdbe.org/1n2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [https://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2s ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/dTDP~~-4-~~dehydrorhamnose_reductase dTDP~~-4-~~dehydrorhamnose reductase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133]~~ </~~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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [~~http~~://pdbe.org/1n2s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2s ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.	+	[https://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		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=1n2s 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=1n2s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from Salmonella enterica serovar Typhimurium has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose are reported. RmlD differs from other short chain dehydrogenases in that it has a novel dimer interface that contains Mg2+. Enzyme catalysis involves hydride transfer from the nicotinamide ring of the cofactor to the C4'-carbonyl group of the substrate. The substrate is activated through protonation by a conserved tyrosine. NAD(P)H is bound in a solvent-exposed cleft, allowing facile replacement. We suggest a novel role for the conserved serine/threonine residue of the catalytic triad of SDR enzymes.
-
-	Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.,Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH Structure. 2002 Jun;10(6):773-86. PMID:12057193<ref>PMID:12057193</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1n2s" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~DTDP-4-dehydrorhamnose reductase~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: Blankenfeldt, W]]	+	[[Category: Blankenfeldt W]]
-	[[Category: Giraud~~, M F~~]]	+	[[Category: Giraud MF]]
-	[[Category: Graninger, M]]	+	[[Category: Graninger M]]
-	[[Category: Kerr~~, I D~~]]	+	[[Category: Kerr ID]]
-	[[Category: Leonard~~, G A~~]]	+	[[Category: Leonard GA]]
-	[[Category: Mcmiken~~, H J~~]]	+	[[Category: Mcmiken HJ]]
-	[[Category: Messner, P]]	+	[[Category: Messner P]]
-	[[Category: Naismith~~, J H~~]]	+	[[Category: Naismith JH]]
-	[[Category: Whitfield, C]]	+	[[Category: Whitfield C]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossman-fold]]~~	+
-	~~[[Category: Sugar-nucleotide-binding domain~~]]	+

OCA at 08:44, 2 December 2020

OCA — Wed, 02 Dec 2020 08:44:14 GMT

←Older revision		Revision as of 08:44, 2 December 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==		==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==
-	<StructureSection load='1n2s' size='340' side='right' caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1n2s' size='340' side='right'caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1N2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1N2S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://pdbe.org/1n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2s 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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://pdbe.org/1n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus typhimurium loeffler 1892]]		[[Category: Bacillus typhimurium loeffler 1892]]
		+	[[Category: Large Structures]]
	[[Category: DTDP-4-dehydrorhamnose reductase]]		[[Category: DTDP-4-dehydrorhamnose reductase]]
	[[Category: Blankenfeldt, W]]		[[Category: Blankenfeldt, W]]

OCA at 08:04, 31 January 2018

OCA — Wed, 31 Jan 2018 08:04:33 GMT

←Older revision		Revision as of 08:04, 31 January 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==		==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==
	<StructureSection load='1n2s' size='340' side='right' caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1n2s' size='340' side='right' caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://pdbe.org/1n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s 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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://pdbe.org/1n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/1n2s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/1n2s_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 15:31, 9 February 2016

OCA — Tue, 09 Feb 2016 15:31:10 GMT

←Older revision		Revision as of 15:31, 9 February 2016
Line 19:		Line 19:
	<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=1n2s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:36, 10 September 2015

OCA — Thu, 10 Sep 2015 23:36:24 GMT

←Older revision		Revision as of 23:36, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1n2s' size='340' side='right' caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1n2s' size='340' side='right' caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar~~ typhimurium]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N2S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 ~~Salmonella enterica subsp. enterica serovar Typhimurium~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s 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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://pdbe.org/1n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1n2s" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salmonella enterica subsp. enterica serovar~~ typhimurium]]	+	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: DTDP-4-dehydrorhamnose reductase]]		[[Category: DTDP-4-dehydrorhamnose reductase]]
	[[Category: Blankenfeldt, W]]		[[Category: Blankenfeldt, W]]

OCA at 07:44, 25 December 2014

OCA — Thu, 25 Dec 2014 07:44:47 GMT

←Older revision		Revision as of 07:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N2S FirstGlance]. <br>		<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N2S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s 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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: DTDP-4-dehydrorhamnose reductase]]		[[Category: DTDP-4-dehydrorhamnose reductase]]
-	[[Category: Blankenfeldt, W.]]	+	[[Category: Blankenfeldt, W]]
-	[[Category: Giraud, M F.]]	+	[[Category: Giraud, M F]]
-	[[Category: Graninger, M.]]	+	[[Category: Graninger, M]]
-	[[Category: Kerr, I D.]]	+	[[Category: Kerr, I D]]
-	[[Category: Leonard, G A.]]	+	[[Category: Leonard, G A]]
-	[[Category: Mcmiken, H J.]]	+	[[Category: Mcmiken, H J]]
-	[[Category: Messner, P.]]	+	[[Category: Messner, P]]
-	[[Category: Naismith, J H.]]	+	[[Category: Naismith, J H]]
-	[[Category: Whitfield, C.]]	+	[[Category: Whitfield, C]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossman-fold]]		[[Category: Rossman-fold]]
	[[Category: Sugar-nucleotide-binding domain]]		[[Category: Sugar-nucleotide-binding domain]]

OCA at 05:31, 3 October 2014

OCA — Fri, 03 Oct 2014 05:31:29 GMT

←Older revision		Revision as of 05:31, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1n2s\| PDB=1n2s \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==
-	===CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH===	+	<StructureSection load='1n2s' size='340' side='right' caption='[[1n2s]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12057193}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N2S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kbz\|1kbz]], [[1kc1\|1kc1]], [[1kc3\|1kc3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [http://www.ebi.ac.uk/pdbsum/1n2s 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/n2/1n2s_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 ==
		+	dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from Salmonella enterica serovar Typhimurium has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose are reported. RmlD differs from other short chain dehydrogenases in that it has a novel dimer interface that contains Mg2+. Enzyme catalysis involves hydride transfer from the nicotinamide ring of the cofactor to the C4'-carbonyl group of the substrate. The substrate is activated through protonation by a conserved tyrosine. NAD(P)H is bound in a solvent-exposed cleft, allowing facile replacement. We suggest a novel role for the conserved serine/threonine residue of the catalytic triad of SDR enzymes.

-	~~==Function==~~	+	Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.,Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH Structure. 2002 Jun;10(6):773-86. PMID:12057193<ref>PMID:12057193</ref>
-	~~[[http://www~~.~~uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY]] Catalyzes the reduction of~~ dTDP-6-deoxy-L-lyxo-4-hexulose ~~to yield dTDP~~-L-~~rhamnose. RmlD uses NADH and NADPH nearly equally well~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1n2s]] is~~ a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. This structure supersedes the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:012057193</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: DTDP-4-dehydrorhamnose reductase]]		[[Category: DTDP-4-dehydrorhamnose reductase]]

OCA at 06:18, 6 November 2013

OCA — Wed, 06 Nov 2013 06:18:49 GMT

←Older revision		Revision as of 06:18, 6 November 2013
Line 4:		Line 4:

	==Function==		==Function==
-	[[http://www.uniprot.org/uniprot/~~RFBD_SALTY RFBD_SALTY~~]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.	+	[[http://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.

	==About this Structure==		==About this Structure==

OCA at 08:44, 27 March 2013

OCA — Wed, 27 Mar 2013 08:44:20 GMT

←Older revision		Revision as of 08:44, 27 March 2013
Line 2:		Line 2:
	===CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH===		===CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH===
	{{ABSTRACT_PUBMED_12057193}}		{{ABSTRACT_PUBMED_12057193}}
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/RFBD_SALTY RFBD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.

	==About this Structure==		==About this Structure==
Line 7:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012057193</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012057193</ref><references group="xtra"/><references/>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: DTDP-4-dehydrorhamnose reductase]]		[[Category: DTDP-4-dehydrorhamnose reductase]]

OCA at 10:23, 13 March 2013

OCA — Wed, 13 Mar 2013 10:23:53 GMT

←Older revision		Revision as of 10:23, 13 March 2013
Line 1:		Line 1:
-	[[Image:1n2s.png\|left\|200px]]
-
	{{STRUCTURE_1n2s\| PDB=1n2s \| SCENE= }}		{{STRUCTURE_1n2s\| PDB=1n2s \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH===		===CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH===
-
	{{ABSTRACT_PUBMED_12057193}}		{{ABSTRACT_PUBMED_12057193}}