PDBsum entry 4zqc

Lyase/lyase inhibitor

PDB id: 4zqc

Contents

Protein chains

268 a.a.

396 a.a.

Ligands

F6F ×3

DMS ×12

PLP

Metals

_NA

Waters ×869

PDB id:

4zqc

Name:

Lyase/lyase inhibitor

Title:

Tryptophan synthase from salmonella typhimurium in complex with two molecules of n-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (f6f) inhibitor in the alpha-site and a single f6f molecule in the beta-site at 1.54 angstrom resolution.

Structure:

Tryptophan synthase alpha chain. Chain: a. Engineered: yes. Tryptophan synthase beta chain. Chain: b. Engineered: yes

Source:

Salmonella enterica subsp. Enterica serovar typhimurium. Organism_taxid: 90371. Gene: trpa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: trpb.

Resolution:

1.54Å R-factor: 0.138 R-free: 0.187

Authors:

E.Hilario,B.G.Caulkins,R.P.Young,M.F.Dunn,L.J.Mueller,L.Fan

Key ref:

E.Hilario et al. (2016). 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. PubMed id: 26708480 DOI: 10.1016/j.bbapap.2015.12.006

Date:

08-May-15 Release date: 10-Feb-16

Protein chain

P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 268 a.a.

Struc: 268 a.a.

Protein chain

P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 397 a.a.

Struc: 396 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.4.2.1.20 - tryptophan synthase.
• Pathway: Tryptophan Biosynthesis
• Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.bbapap.2015.12.006

Biochim Biophys Acta 1864:268-279 (2016)

PubMed id: 26708480

Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water.

E.Hilario, B.G.Caulkins, Y.M.Huang, W.You, C.E.Chang, L.J.Mueller, M.F.Dunn, L.Fan.

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.