4WX2

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with two F6F molecules in the alpha-site and one F6F molecule in the beta-site

Summary for 4WX2

• Entry DOI: 10.2210/pdb4wx2/pdb
• Related: 2CLE 2CLF 2CLM 4KKX
• Descriptor: Tryptophan synthase alpha chain, Tryptophan synthase beta chain, 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE, ... (8 entities in total)
• Functional Keywords: carbon-oxygen lyase, tryptophan biosynthesis, salmonella typhimurium, f6f, inhibitor, allosteric enzyme, aromatic amino acid biosynthesis, pyridoxal phosphate, transferase
• Biological source: Salmonella enterica subsp. enterica serovar Typhimurium; More
• Total number of polymer chains: 2
• Total formula weight: 73043.49

Authors

Hilario, E.,Caulkins, B.G.,Young, R.P.,Niks, D.,Dunn, M.F.,Mueller, L.J.,Fan, L. (deposition date: 2014-11-13, release date: 2015-11-18, Last modification date: 2023-09-27)

Primary citation

Hilario, E.,Caulkins, B.G.,Huang, Y.M.,You, W.,Chang, C.E.,Mueller, L.J.,Dunn, M.F.,Fan, L.
Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water.
Biochim.Biophys.Acta, 1864:268-279, 2016

PubMed Abstract: Four new X-ray structures of tryptophan synthase (TS) crystallized with varying numbers of the amphipathic N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) molecule are presented. These structures show one of the F6 ligands threaded into the tunnel from the β-site and reveal a distinct hydrophobic region. Over this expanse, the interactions between F6 and the tunnel are primarily nonpolar, while the F6 phosphoryl group fits into a polar pocket of the β-subunit active site. Further examination of TS structures reveals that one portion of the tunnel (T1) binds clusters of water molecules, whereas waters are not observed in the nonpolar F6 binding region of the tunnel (T2). MD simulation of another TS structure with an unobstructed tunnel also indicates the T2 region of the tunnel excludes water, consistent with a dewetted state that presents a significant barrier to the transfer of water into the closed β-site. We conclude that hydrophobic molecules can freely diffuse between the α- and β-sites via the tunnel, while water does not. We propose that exclusion of water serves to inhibit reaction of water with the α-aminoacrylate intermediate to form ammonium ion and pyruvate, a deleterious side reaction in the αβ-catalytic cycle. Finally, while most TS structures show βPhe280 partially blocking the tunnel between the α- and β-sites, new structures show an open tunnel, suggesting the flexibility of the βPhe280 side chain. Flexible docking studies and MD simulations confirm that the dynamic behavior of βPhe280 allows unhindered transfer of indole through the tunnel, therefore excluding a gating role for this residue.

PubMed: 26708480
DOI: 10.1016/j.bbapap.2015.12.006

Experimental method

X-RAY DIFFRACTION (1.75 Å)