3PR2

Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site

Summary for 3PR2

• Entry DOI: 10.2210/pdb3pr2/pdb
• Descriptor: Tryptophan synthase alpha chain, Tryptophan synthase beta chain, 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE, ... (6 entities in total)
• Functional Keywords: alpha-beta barrel, tim-barrel, tryptophan synthesis, lyase
• Biological source: Salmonella enterica subsp. enterica serovar Typhimurium; More
• Total number of polymer chains: 2
• Total formula weight: 71926.89

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. (deposition date: 2010-11-29, release date: 2011-02-09, Last modification date: 2024-02-21)

Primary citation

Lai, J.,Niks, D.,Wang, Y.,Domratcheva, T.,Barends, T.R.,Schwarz, F.,Olsen, R.A.,Elliott, D.W.,Fatmi, M.Q.,Chang, C.E.,Schlichting, I.,Dunn, M.F.,Mueller, L.J.
X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase.
J.Am.Chem.Soc., 133:4-7, 2011

PubMed Abstract: 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.

PubMed: 21142052
DOI: 10.1021/ja106555c

Experimental method

X-RAY DIFFRACTION (1.85 Å)