3box - Revision history

OCA at 12:11, 30 August 2023

2023-08-30T12:11:36Z

← Older revision		Revision as of 12:11, 30 August 2023
Line 1:		Line 1:

	==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==		==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==
	<StructureSection load='3box' size='340' side='right'caption='[[3box]]' scene=''>		<StructureSection load='3box' size='340' side='right'caption='[[3box]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BOX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3box]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BOX FirstGlance]. <br>
	</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [https://pdbe.org/3box PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [https://www.ebi.ac.uk/pdbsum/3box PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3box ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></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]] 1.8Å</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></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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [https://pdbe.org/3box PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [https://www.ebi.ac.uk/pdbsum/3box PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3box ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/RHMD_SALTY RHMD_SALTY] Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.<ref>PMID:18754693</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		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=3box 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=3box ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The l-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by the genome of Escherichia coli K-12. We screened a library of acid sugars to discover that the enzyme displays a promiscuous substrate specificity: l-rhamnonate (6-deoxy- l-mannonate) has the "best" kinetic constants, with l-mannonate, l-lyxonate, and d-gulonate dehydrated less efficiently. Crystal structures of the RhamDs from both E. coli K-12 and Salmonella typhimurium LT2 (95% sequence identity) were obtained in the presence of Mg (2+); the structure of the RhamD from S. typhimurium was also obtained in the presence of 3-deoxy- l-rhamnonate (obtained by reduction of the product with NaBH 4). Like other members of the enolase superfamily, RhamD contains an N-terminal alpha + beta capping domain and a C-terminal (beta/alpha) 7beta-barrel (modified TIM-barrel) catalytic domain with the active site located at the interface between the two domains. In contrast to other members, the specificity-determining "20s loop" in the capping domain is extended in length and the "50s loop" is truncated. The ligands for the Mg (2+) are Asp 226, Glu 252 and Glu 280 located at the ends of the third, fourth and fifth beta-strands, respectively. The active site of RhamD contains a His 329-Asp 302 dyad at the ends of the seventh and sixth beta-strands, respectively, with His 329 positioned to function as the general base responsible for abstraction of the C2 proton of l-rhamnonate to form a Mg (2+)-stabilized enediolate intermediate. However, the active site does not contain other acid/base catalysts that have been implicated in the reactions catalyzed by other members of the MR subgroup of the enolase superfamily. Based on the structure of the liganded complex, His 329 also is expected to function as the general acid that both facilitates departure of the 3-OH group in a syn-dehydration reaction and delivers a proton to carbon-3 to replace the 3-OH group with retention of configuration.

			Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.,Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:18754693<ref>PMID:18754693</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 3box" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
			[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
	[[Category: Almo SC]]		[[Category: Almo SC]]
	[[Category: Burley SK]]		[[Category: Burley SK]]

OCA at 08:20, 19 January 2022

2022-01-19T08:20:53Z

← Older revision		Revision as of 08:20, 19 January 2022
Line 1:		Line 1:

	==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==		==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==
	<StructureSection load='3box' size='340' side='right' caption='[[3box]]~~, [[Resolution\|resolution]] 1.80Å~~' scene=''>		<StructureSection load='3box' size='340' side='right'caption='[[3box]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BOX FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BOX 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></td></tr>~~		</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [https://pdbe.org/3box PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [https://www.ebi.ac.uk/pdbsum/3box PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3box ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>~~
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [~~http~~://pdbe.org/3box PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3box PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3box ProSAT], [~~http~~://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[http://www.uniprot.org/uniprot/RHMD_SALTY RHMD_SALTY]] Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.<ref>PMID:18754693</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 16:
	</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=3box 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=3box ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The l-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by the genome of Escherichia coli K-12. We screened a library of acid sugars to discover that the enzyme displays a promiscuous substrate specificity: l-rhamnonate (6-deoxy- l-mannonate) has the "best" kinetic constants, with l-mannonate, l-lyxonate, and d-gulonate dehydrated less efficiently. Crystal structures of the RhamDs from both E. coli K-12 and Salmonella typhimurium LT2 (95% sequence identity) were obtained in the presence of Mg (2+); the structure of the RhamD from S. typhimurium was also obtained in the presence of 3-deoxy- l-rhamnonate (obtained by reduction of the product with NaBH 4). Like other members of the enolase superfamily, RhamD contains an N-terminal alpha + beta capping domain and a C-terminal (beta/alpha) 7beta-barrel (modified TIM-barrel) catalytic domain with the active site located at the interface between the two domains. In contrast to other members, the specificity-determining "20s loop" in the capping domain is extended in length and the "50s loop" is truncated. The ligands for the Mg (2+) are Asp 226, Glu 252 and Glu 280 located at the ends of the third, fourth and fifth beta-strands, respectively. The active site of RhamD contains a His 329-Asp 302 dyad at the ends of the seventh and sixth beta-strands, respectively, with His 329 positioned to function as the general base responsible for abstraction of the C2 proton of l-rhamnonate to form a Mg (2+)-stabilized enediolate intermediate. However, the active site does not contain other acid/base catalysts that have been implicated in the reactions catalyzed by other members of the MR subgroup of the enolase superfamily. Based on the structure of the liganded complex, His 329 also is expected to function as the general acid that both facilitates departure of the 3-OH group in a syn-dehydration reaction and delivers a proton to carbon-3 to replace the 3-OH group with retention of configuration.

	Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.,Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:18754693<ref>PMID:18754693</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3box" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Salty~~]]		[[Category: Large Structures]]
	[[Category: Almo~~, S C~~]]		[[Category: Almo SC]]
	[[Category: Burley~~, S K~~]]		[[Category: Burley SK]]
	[[Category: Fedorov~~, A A~~]]		[[Category: Fedorov AA]]
	[[Category: Fedorov~~, E V~~]]		[[Category: Fedorov EV]]
	[[Category: Gerlt~~, J A]]~~		[[Category: Gerlt JA]]
	~~[[Category: Structural genomic~~]]		[[Category: Sauder JM]]
	[[Category: Sauder~~, J M]]~~
	~~[[Category: Clone name 9265a2bst6p1]]~~
	~~[[Category: L-rhamnonate dehydratase]]~~
	~~[[Category: Lyase]]~~
	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~
	~~[[Category: PSI, Protein structure initiative]]~~
	~~[[Category: Target 9265a~~]]

OCA at 08:12, 31 October 2018

2018-10-31T08:12:39Z

← Older revision		Revision as of 08:12, 31 October 2018
Line 1:		Line 1:

	==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==		==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==
	<StructureSection load='3box' size='340' side='right' caption='[[3box]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3box' size='340' side='right' caption='[[3box]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://pdbe.org/3box PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://pdbe.org/3box PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3box ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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/bo/3box_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bo/3box_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 19:29, 7 February 2016

2016-02-07T19:29:19Z

← Older revision		Revision as of 19:29, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3box' size='340' side='right' caption='[[3box]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3box' size='340' side='right' caption='[[3box]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOX 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 ~~Salmonella enterica subsp. enterica serovar Typhimurium str. LT2~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://pdbe.org/3box PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RHMD_SALTY RHMD_SALTY]] Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.<ref>PMID:18754693</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		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=3box ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		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 3box" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Salmonella enterica subsp. enterica serovar typhimurium str. lt2~~]]		[[Category: Salty]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]

OCA at 12:56, 6 November 2014

2014-11-06T12:56:01Z

← Older revision		Revision as of 12:56, 6 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOX FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2])</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K]]
	[[Category: Fedorov, A A.]]		[[Category: Fedorov, A A]]
	[[Category: Fedorov, E V.]]		[[Category: Fedorov, E V]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A]]
	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]		[[Category: Structural genomic]]
	[[Category: Sauder, J M.]]		[[Category: Sauder, J M]]
	[[Category: Clone name 9265a2bst6p1]]		[[Category: Clone name 9265a2bst6p1]]
	[[Category: L-rhamnonate dehydratase]]		[[Category: L-rhamnonate dehydratase]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~		[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
	~~[[Category: Nysgxrc~~]]		[[Category: PSI, Protein structure initiative]]
	[[Category: Protein structure initiative]]
	~~[[Category: Psi-2]]~~
	~~[[Category: Structural genomic~~]]
	[[Category: Target 9265a]]		[[Category: Target 9265a]]

OCA at 21:28, 2 October 2014

2014-10-02T21:28:08Z

← Older revision		Revision as of 21:28, 2 October 2014
Line 1:		Line 1:
	[[Image:~~3box~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg==
			<StructureSection load='3box' size='340' side='right' caption='[[3box]], [[Resolution\|resolution]] 1.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOX FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsh\|2gsh]], [[2p3z\|2p3z]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfaW, STM2291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2])</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=3box FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3box OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3box RCSB], [http://www.ebi.ac.uk/pdbsum/3box PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/3box TOPSAN]</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/bo/3box_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 ==
			The l-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by the genome of Escherichia coli K-12. We screened a library of acid sugars to discover that the enzyme displays a promiscuous substrate specificity: l-rhamnonate (6-deoxy- l-mannonate) has the "best" kinetic constants, with l-mannonate, l-lyxonate, and d-gulonate dehydrated less efficiently. Crystal structures of the RhamDs from both E. coli K-12 and Salmonella typhimurium LT2 (95% sequence identity) were obtained in the presence of Mg (2+); the structure of the RhamD from S. typhimurium was also obtained in the presence of 3-deoxy- l-rhamnonate (obtained by reduction of the product with NaBH 4). Like other members of the enolase superfamily, RhamD contains an N-terminal alpha + beta capping domain and a C-terminal (beta/alpha) 7beta-barrel (modified TIM-barrel) catalytic domain with the active site located at the interface between the two domains. In contrast to other members, the specificity-determining "20s loop" in the capping domain is extended in length and the "50s loop" is truncated. The ligands for the Mg (2+) are Asp 226, Glu 252 and Glu 280 located at the ends of the third, fourth and fifth beta-strands, respectively. The active site of RhamD contains a His 329-Asp 302 dyad at the ends of the seventh and sixth beta-strands, respectively, with His 329 positioned to function as the general base responsible for abstraction of the C2 proton of l-rhamnonate to form a Mg (2+)-stabilized enediolate intermediate. However, the active site does not contain other acid/base catalysts that have been implicated in the reactions catalyzed by other members of the MR subgroup of the enolase superfamily. Based on the structure of the liganded complex, His 329 also is expected to function as the general acid that both facilitates departure of the 3-OH group in a syn-dehydration reaction and delivers a proton to carbon-3 to replace the 3-OH group with retention of configuration.

	~~{{STRUCTURE_3box\| PDB=3box \| SCENE= }}~~		Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.,Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:18754693<ref>PMID:18754693</ref>

	~~===Crystal structure~~ of ~~L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18754693}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3box]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Salmonella_enterica_subsp~~.~~_enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018754693<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

OCA: Protected "3box" [edit=sysop:move=sysop]

2013-01-07T18:18:31Z

Protected "3box" [edit=sysop:move=sysop]

← Older revision	Revision as of 18:18, 7 January 2013
(No difference)

OCA at 18:18, 7 January 2013

2013-01-07T18:18:27Z

← Older revision		Revision as of 18:18, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:3box.png\|left\|200px]]		[[Image:3box.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3box", 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_3box\| PDB=3box \| SCENE= }}		{{STRUCTURE_3box\| PDB=3box \| SCENE= }}

	===Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg===		===Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18754693}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18754693 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18754693}}		{{ABSTRACT_PUBMED_18754693}}

	==About this Structure==		==About this Structure==
	~~3BOX~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Salmonella_typhimurium_lt2~~ Salmonella typhimurium lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA].		[[3box]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18754693~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018754693</ref><references group="xtra"/>
	[[Category: Salmonella typhimurium lt2]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]
Line 41:		Line 29:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Target 9265a]]		[[Category: Target 9265a]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:01:45 2009''~~

OCA at 14:01, 16 February 2009

2009-02-16T14:01:46Z

← Older revision		Revision as of 14:01, 16 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
	Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase., Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA, Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~18754693 18754693]~~		<ref group="xtra">PMID:18754693</ref><references group="xtra"/>
	[[Category: Salmonella typhimurium lt2]]		[[Category: Salmonella typhimurium lt2]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
Line 42:		Line 42:
	[[Category: Target 9265a]]		[[Category: Target 9265a]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov~~ 16 10:31:~~40 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:01:45 2009''

OCA at 08:31, 16 November 2008

2008-11-16T08:31:42Z

← Older revision		Revision as of 08:31, 16 November 2008
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3BOX is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Salmonella_typhimurium_lt2 Salmonella typhimurium lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA].		3BOX is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Salmonella_typhimurium_lt2 Salmonella typhimurium lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOX OCA].

	==Reference==		==Reference==
	Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase., Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA, Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18754693 18754693]		Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase., Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA, Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18754693 18754693]
	[[Category: Salmonella typhimurium lt2]]		[[Category: Salmonella typhimurium lt2]]
	~~[[Category: Single protein]]~~
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]
Line 43:		Line 42:
	[[Category: Target 9265a]]		[[Category: Target 9265a]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Sep 24 09~~:00:36 2008''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 10:31:40 2008''