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==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=''> | |||
{{ | == 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. | |||
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> | |||
==See Also== | ==See Also== | ||
*[[Tryptophan synthase|Tryptophan synthase]] | *[[Tryptophan synthase|Tryptophan synthase]] | ||
== References == | |||
== | <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]] | ||
Revision as of 13:56, 19 December 2014
Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha siteTryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site
Structural highlights
Publication Abstract from PubMedChemical-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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