Crystal Structure of E. coli Tryptophanase in “Semi-Holo” Form: An Insight into Allostery of the Enzyme

Abstract

A new crystal form of E. coli tryptophanase (tryptophan indole-lyase, Trpase) (space group P43212, a=b=109.97 A, c=238.40 A) was obtained under the same conditions as the tetragonal crystals of holo E. coli. Trpase. The structure was solved by molecular replacement at 3.2 A resolution using the coordinates of apo E. coli Trpase (PDB code 2OQX) as a search model and refined to R=21.3 %, Rfree=28.9 %. Out of two polypeptide chains contained in the asymmetric unit, one was found in holo form with PLP covalently attached to Lys271, while the other appeared to be in the apo form. The overall conformation of the holo subunit is the same as in the holo form of tyrosine phenol-lyase. The apo subunit is found in a wide-open conformation very similar to the one observed in the crystal structure of apo Trpase. Taking into account the flexibility of apo Trpase as seen in the known structures and difference in the crystallization conditions (pH, precipitant) and crystal packing, this finding is quite unexpected. We suggest that apo Trpase is found in the solution predominantly in the wide-open conformation which partially closes upon binding of PLP. The closed conformation might correspond to the enzyme state with both cofactor and substrate bound, in a way similar to tyrosine phenol-lyase. In addition, the conformation of the loop 301-310 is different in apo and holo subunits of the new structure suggesting that this conformational change is not induced by the oxidation of Cys298.