3pr2 - Revision history

OCA at 10:42, 21 February 2024

2024-02-21T10:42:41Z

← Older revision		Revision as of 10:42, 21 February 2024
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	<StructureSection load='3pr2' size='340' side='right'caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3pr2' size='340' side='right'caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</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]] 1.85Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STM1727, trpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), STM1726, trpB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [https://pdbe.org/3pr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [https://www.ebi.ac.uk/pdbsum/3pr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pr2 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [https://pdbe.org/3pr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [https://www.ebi.ac.uk/pdbsum/3pr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pr2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. ~~[[https://www.uniprot.org/uniprot/TRPB_SALTY TRPB_SALTY]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.~~		[https://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Chemical-level details such as protonation and hybridization state are critical for understanding enzyme mechanism and function. Even at high resolution, these details are difficult to determine by X-ray crystallography alone. The chemical shift in NMR spectroscopy, however, is an extremely sensitive probe of the chemical environment, making solid-state NMR spectroscopy and X-ray crystallography a powerful combination for defining chemically detailed three-dimensional structures. Here we adopted this combined approach to determine the chemically rich crystal structure of the indoline quinonoid intermediate in the pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase under conditions of active catalysis. Models of the active site were developed using a synergistic approach in which the structure of this reactive substrate analogue was optimized using ab initio computational chemistry in the presence of side-chain residues fixed at their crystallographically determined coordinates. Various models of charge and protonation state for the substrate and nearby catalytic residues could be uniquely distinguished by their calculated effects on the chemical shifts measured at specifically (13)C- and (15)N-labeled positions on the substrate. Our model suggests the importance of an equilibrium between tautomeric forms of the substrate, with the protonation state of the major isomer directing the next catalytic step.

	X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase.,Lai J, Niks D, Wang Y, Domratcheva T, Barends TR, Schwarz F, Olsen RA, Elliott DW, Fatmi MQ, Chang CE, Schlichting I, Dunn MF, Mueller LJ J Am Chem Soc. 2011 Jan 12;133(1):4-7. Epub 2010 Dec 10. PMID:21142052<ref>PMID:21142052</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3pr2" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Tryptophan synthase 3D structures\|Tryptophan synthase 3D structures]]		*[[Tryptophan synthase 3D structures\|Tryptophan synthase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Bacillus typhimurium loeffler 1892]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Tryptophan synthase~~]]		[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
	[[Category: Barends~~, T R.M~~]]		[[Category: Barends TRM]]
	[[Category: Chang~~, C A~~]]		[[Category: Chang CA]]
	[[Category: Domratcheva, T]]		[[Category: Domratcheva T]]
	[[Category: Dunn~~, M F~~]]		[[Category: Dunn MF]]
	[[Category: Elliott~~, D W~~]]		[[Category: Elliott DW]]
	[[Category: Fatmi~~, M Q~~]]		[[Category: Fatmi MQ]]
	[[Category: Lai, J]]		[[Category: Lai J]]
	[[Category: Mueller~~, L J~~]]		[[Category: Mueller LJ]]
	[[Category: Niks, D]]		[[Category: Niks D]]
	[[Category: Olsen~~, R A~~]]		[[Category: Olsen RA]]
	[[Category: Schlichting, I]]		[[Category: Schlichting I]]
	[[Category: Schwarz, F]]		[[Category: Schwarz F]]
	[[Category: Wang, Y]]		[[Category: Wang Y]]
	~~[[Category: Alpha-beta barrel]]~~
	~~[[Category: Lyase]]~~
	~~[[Category: Tim-barrel]]~~
	~~[[Category: Tryptophan synthesis~~]]

OCA at 08:51, 25 May 2022

2022-05-25T08:51:20Z

← Older revision		Revision as of 08:51, 25 May 2022
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	<StructureSection load='3pr2' size='340' side='right'caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3pr2' size='340' side='right'caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STM1727, trpA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), STM1726, trpB ([~~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">STM1727, trpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), STM1726, trpB ([https://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/Tryptophan_synthase Tryptophan synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [~~http~~://pdbe.org/3pr2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pr2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pr2 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [https://pdbe.org/3pr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [https://www.ebi.ac.uk/pdbsum/3pr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pr2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. [[~~http~~://www.uniprot.org/uniprot/TRPB_SALTY TRPB_SALTY]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.		[[https://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. [[https://www.uniprot.org/uniprot/TRPB_SALTY TRPB_SALTY]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Tryptophan synthase\|Tryptophan synthase]]		*[[Tryptophan synthase 3D structures\|Tryptophan synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:32, 17 July 2019

2019-07-17T11:32:41Z

← Older revision		Revision as of 11:32, 17 July 2019
Line 1:		Line 1:

	==Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site==		==Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site==
	<StructureSection load='3pr2' size='340' side='right' caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3pr2' size='340' side='right'caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3pr2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pr2" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Tryptophan synthase\|Tryptophan synthase]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus typhimurium loeffler 1892]]		[[Category: Bacillus typhimurium loeffler 1892]]
			[[Category: Large Structures]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
	[[Category: Barends, T R.M]]		[[Category: Barends, T R.M]]

OCA at 09:05, 8 November 2017

2017-11-08T09:05:55Z

← Older revision		Revision as of 09:05, 8 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3pr2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pr2" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Tryptophan synthase\|Tryptophan synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:10, 5 August 2016

2016-08-05T10:10:26Z

← Older revision		Revision as of 10:10, 5 August 2016
Line 1:		Line 1:

	==Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site==		==Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site==
	<StructureSection load='3pr2' size='340' side='right' caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3pr2' size='340' side='right' caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar~~ typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STM1727, trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 ~~Salmonella enterica subsp. enterica serovar Typhimurium~~]), STM1726, trpB ([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">STM1727, trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), STM1726, trpB ([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/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [http://www.ebi.ac.uk/pdbsum/3pr2 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=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [http://pdbe.org/3pr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [http://www.ebi.ac.uk/pdbsum/3pr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pr2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3pr2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Salmonella enterica subsp. enterica serovar~~ typhimurium]]		[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
	[[Category: Barends, T R.M]]		[[Category: Barends, T R.M]]

OCA at 01:28, 25 December 2014

2014-12-25T01:28:44Z

← Older revision		Revision as of 01:28, 25 December 2014
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	<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=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [http://www.ebi.ac.uk/pdbsum/3pr2 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=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [http://www.ebi.ac.uk/pdbsum/3pr2 PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. [[http://www.uniprot.org/uniprot/TRPB_SALTY TRPB_SALTY]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:56, 19 December 2014

2014-12-19T10:56:33Z

← Older revision		Revision as of 10:56, 19 December 2014
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	~~{{STRUCTURE_3pr2\| PDB=3pr2 \| SCENE= }}~~		==Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site==
	===Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site===		<StructureSection load='3pr2' size='340' side='right' caption='[[3pr2]], [[Resolution\|resolution]] 1.85Å' scene=''>
	{{~~ABSTRACT_PUBMED_21142052}~~}		== Structural highlights ==
			<table><tr><td colspan='2'>[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PR2 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MN:(Z)-N-[(1E)-1-CARBOXY-2-(2,3-DIHYDRO-1H-INDOL-1-YL)ETHYLIDENE]{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHANAMINIUM'>7MN</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=F9F:2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL+DIHYDROGEN+PHOSPHATE'>F9F</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STM1727, trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium]), STM1726, trpB ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=3pr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pr2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pr2 RCSB], [http://www.ebi.ac.uk/pdbsum/3pr2 PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Chemical-level details such as protonation and hybridization state are critical for understanding enzyme mechanism and function. Even at high resolution, these details are difficult to determine by X-ray crystallography alone. The chemical shift in NMR spectroscopy, however, is an extremely sensitive probe of the chemical environment, making solid-state NMR spectroscopy and X-ray crystallography a powerful combination for defining chemically detailed three-dimensional structures. Here we adopted this combined approach to determine the chemically rich crystal structure of the indoline quinonoid intermediate in the pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase under conditions of active catalysis. Models of the active site were developed using a synergistic approach in which the structure of this reactive substrate analogue was optimized using ab initio computational chemistry in the presence of side-chain residues fixed at their crystallographically determined coordinates. Various models of charge and protonation state for the substrate and nearby catalytic residues could be uniquely distinguished by their calculated effects on the chemical shifts measured at specifically (13)C- and (15)N-labeled positions on the substrate. Our model suggests the importance of an equilibrium between tautomeric forms of the substrate, with the protonation state of the major isomer directing the next catalytic step.

	~~==Function==~~		X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase.,Lai J, Niks D, Wang Y, Domratcheva T, Barends TR, Schwarz F, Olsen RA, Elliott DW, Fatmi MQ, Chang CE, Schlichting I, Dunn MF, Mueller LJ J Am Chem Soc. 2011 Jan 12;133(1):4-7. Epub 2010 Dec 10. PMID:21142052<ref>PMID:21142052</ref>
	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/TRPA_SALTY TRPA_SALTY]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3~~-~~phosphate~~. ~~[[http~~:/~~/www.uniprot.org/uniprot/TRPB_SALTY TRPB_SALTY]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.~~

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[3pr2]] is~~ a ~~2 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Salmonella_enterica_subsp~~.~~_enterica_serovar_typhimurium Salmonella enterica subsp~~. ~~enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin~~/~~ocashort?id=3PR2 OCA].~~		</div>

	==See Also==		==See Also==
	*[[Tryptophan synthase\|Tryptophan synthase]]		*[[Tryptophan synthase\|Tryptophan synthase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:021142052</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
	[[Category: Barends, T R.M.]]		[[Category: Barends, T R.M]]
	[[Category: Chang, C A.]]		[[Category: Chang, C A]]
	[[Category: Domratcheva, T.]]		[[Category: Domratcheva, T]]
	[[Category: Dunn, M F.]]		[[Category: Dunn, M F]]
	[[Category: Elliott, D W.]]		[[Category: Elliott, D W]]
	[[Category: Fatmi, M Q.]]		[[Category: Fatmi, M Q]]
	[[Category: Lai, J.]]		[[Category: Lai, J]]
	[[Category: Mueller, L J.]]		[[Category: Mueller, L J]]
	[[Category: Niks, D.]]		[[Category: Niks, D]]
	[[Category: Olsen, R A.]]		[[Category: Olsen, R A]]
	[[Category: Schlichting, I.]]		[[Category: Schlichting, I]]
	[[Category: Schwarz, F.]]		[[Category: Schwarz, F]]
	[[Category: Wang, Y.]]		[[Category: Wang, Y]]
	[[Category: Alpha-beta barrel]]		[[Category: Alpha-beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]
	[[Category: Tryptophan synthesis]]		[[Category: Tryptophan synthesis]]

OCA at 08:22, 8 May 2013

2013-05-08T08:22:30Z

← Older revision		Revision as of 08:22, 8 May 2013
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	~~[[Image:3pr2.jpg\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3pr2", 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_3pr2\| PDB=3pr2 \| SCENE= }}		{{STRUCTURE_3pr2\| PDB=3pr2 \| SCENE= }}

	===Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site===		===Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site===
			{{ABSTRACT_PUBMED_21142052}}

			==Function==
	~~<!--~~		[[http://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. [[http://www.uniprot.org/uniprot/TRPB_SALTY TRPB_SALTY]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.
	The ~~line below this paragraph, {{ABSTRACT_PUBMED_21142052}}, adds~~ the ~~Publication Abstract~~ to ~~the page~~
	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 21142052~~ is the ~~PubMed ID number.~~
	-->
	~~{{ABSTRACT_PUBMED_21142052}}~~

	==About this Structure==		==About this Structure==
	[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA].		[[3pr2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PR2 OCA].

			==See Also==
			*[[Tryptophan synthase\|Tryptophan synthase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~21142052~~</ref><references group="xtra"/>		<ref group="xtra">PMID:021142052</ref><references group="xtra"/><references/>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
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	[[Category: Schwarz, F.]]		[[Category: Schwarz, F.]]
	[[Category: Wang, Y.]]		[[Category: Wang, Y.]]
			[[Category: Alpha-beta barrel]]
			[[Category: Lyase]]
			[[Category: Tim-barrel]]
			[[Category: Tryptophan synthesis]]

OCA: Protected "3pr2" [edit=sysop:move=sysop]

2011-02-09T06:12:46Z

Protected "3pr2" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:12, 9 February 2011
(No difference)

OCA at 06:12, 9 February 2011

2011-02-09T06:12:42Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3pr2.jpg|left|200px]]
-The entry 3pr2 is ON HOLD
+<!--
-Authors: Lai, J., Niks, D., Wang, Y., Domratcheva, T., Barends, T.R.M., Schwarz, F., Olsen, R.A., Elliott, D.W., Fatmi, M.Q., Chang, C.A., Schlichting, I., Dunn, M.F., Mueller, L.J.
+===Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  8 11:33:10 2010''
+<!--