Structure tryptophan binding

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

The trp operon contains a cluster of five structural genes associated with tryptophan biosynthesis. Initiation of transcription of the trp operon is regulated by a repressor protein that functions similarly to the lac repressor. The main difference is that the trp repressor action is subject to control by the small-molecule effector, tryptophan. When tryptophan binds the repressor, the repressor binds to the trp operator. Thus, the effect of the small-molecule effector here is opposite to its effect on the lac operon. When tryptophan is present, there is no need for the enzymes that synthesize tryptophan. 

In all these crystal structures, trp repressor occurs as a dimer with intertwined subunits related by a twofold rotation axis. When tryptophan binds to the apo repressor protein, a conformational change is induced through reorientation of several hydrogen bonds (Fig. 20.19). It rotates the helix/turn/helix motif such that... 

The mechanism of TRAP activation by tryptophan is not known because the structure of nonliganded TRAP (apo-TRAP) has not been determined, although it is known that tryptophan binding is not required for oligomerization of the protein (27). NMR studies of TRAP in both the nonliganded and the activated states demonstrate that apo-TRAP is more flexible than the tryptophan-activated protein (28), which imply that reduced flexibility plays an important role in altering the RNA binding activity of TRAP. 

Sidransky and Verney5 reported that cycloheximide added in vitro diminished 3H-tryptophan binding to hepatic nuclei, probably related to its structural effect on the nuclear receptor. This effect may also occur in vivo, in addition to cycloheximide s action in inhibiting tissue and organ protein synthesis, and may possibly contribute in a minor way to the alteration in tryptophan level in serum. 

Fig. 1.15 Regulation ofthe Trp operon in coli. A) The Trp repressor requires Trp in order to bind its affiliated DNA binding element. In the absence of tryptophan, the Trp repressor can not bind to the regulatory sequence and is therefor inactive. Upon an increase in the tryptohan concentration, tryptophan binds to the Trp repressor and transforms it into a binding-proficient form. The DNA bound Trp repressor prevents the transcription ofthe structural genes, and the biosynthesis of tryptophan is halted. B) structural basis for the activation ofthe...

This clearly emphasizes an important function for threonine M222 and tryptophan M252 in the reaction center structure. Tryptophan M252 mediates binding of to its site presumably via a charge transfer interaction (6) between the electron donor tryptophan and the electron acceptor and thus optimizes reaction center function. This is especially evident in the crystal structure of Rps. viridis were the Ti-electron rich C2-C3 bond of the indole... 

Zhang, R.-G., et al. The crystal structure of trp aporepressor at 1.8 A shows how binding tryptophan enhances DNA affinity. Nature 327 591-S97, 1987. 

Both enzymes belong to the family of a,p-hydrolases." The active site of MeHNL is located inside the protein and connected to the outside through a small channel, which is covered by the bulky amino acid tryptophane 128." It was possible to obtain the crystal structure of the complex with the natural substrate acetone cyanohydrin with the mutant SerSOAla of MeHNL. This complex allowed the determination of the mode of substrate binding in the active site." A summary of 3D structures of known HNLs was published recently." " ... 

The structure of the major trimeric LHCII complex has been recently obtained at 2.72 A (Figure 7.3) (Liu et al., 2004). It was revealed that each 25kDa protein monomer contains three transmembrane and three amphiphilic a-helixes. In addition, each monomer binds 14 chlorophyll (8 Chi a and 6 Chi b) and 4 xanthophyll molecules 1 neoxanthin, 2 luteins, and 1 violaxanthin. The first three xanthophylls are situated close to the integral helixes and are tightly bound to some amino acids by hydrogen bonds to hydroxyl oxygen atoms and van der Waals interactions to chlorophylls, and hydrophobic amino acids such as tryptophan and phenylalanine. 

Gelb, M.H., Cho, W. and Wilton, D.C. (1999) Interfacial binding of secreted phospholipase A2 more than electrostatics and a major role for tryptophan. Current Opinion in Structural Biology 9, 428-432. 

Kennedy, M.W., Scott, J.C., Lo, S.J., Beauchamp, J. and McManus, D.P. (2000) The Sj-FABPc fatty acid binding protein of the human blood fluke Schistosoma japonicum structural and functional characterisation and unusual solvent exposure of a portal-proximal tryptophan. BiochemicalJournal 349, 377-384. 

Sodium periodate also may affect tryptophan residues in some proteins. The oxidation of tryptophan can result in activity losses if the amino acid is an essential component of the active site. For instance, avidin and streptavidin may be severely inactivated by treatment with periodate, since tryptophan is important in forming the biotin-binding pocket. In addition, many other amino acid residues are susceptible to oxidation by periodate (Chapter 1, Section 1.1). Limiting the time of oxidation is important to restricting oxidation to diol groups while not affecting other protein structures. 

B. and Willson, T.M. (2003) X-ray crystal structure of the liver X receptor (> ligand binding domain regulation by a histidine-tryptophan switch. The Journal of Biological Chemistry, 278, 27138-27143. 

---