Crystal structures tryptophane

Figure 3.2. Crystal structures of (upper left) Cu(L-tryptophan)(2,2 bipyridine) CIO 4 (upper right) Cu(L-Tryptophan)(1, l()-phenanthroline)ClO4 . 5H2O and (lower) Cu(L-...

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. 

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. 

Conversely, when A-alkyl tryptophan methyl esters were condensed with aldehydes, the trans diastereomers were observed as the major products." X-ray-crystal structures of 1,2,3-trisubstituted tetrahydro-P-carbolines revealed that the Cl substituent preferentially adopted a pseudo-axial position, forcing the C3 substituent into a pseudo-equatorial orientation to give the kinetically and thermodynamically preferred trans isomer." As the steric size of the Cl and N2 substituents increased, the selectivity for the trans isomer became greater. A-alkyl-L-tryptophan methyl ester 42 was condensed with various aliphatic aldehydes in the presence of trifluoroacetic acid to give predominantly the trans isomers. ... 

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." " ... 

Fig. 6. Backscattered Raman and ROA spectra of native (top pair) and A-state (second pair) bovine G -lactalbumin, and of native (third pair) and A-state (bottom pair) equine lysozyme, together with MOLSCRIPT diagrams of the crystal structures (PDB codes lhfz and 2eql) showing the tryptophans. The native proteins were in acetate buffer at pH 4.6 and 5.6, respectively, and the A-states in glycine buffer at pH 1.9. The native-state and A-state spectra were recorded at 20°C and 2°C, respectively.

The crystal structure of the extracellular domain of P0 has also been determined [41]. The arrangement of molecules in the crystal indicates that P0 may exist on the membrane surface as a tetramer (Fig. 7-7) that can link to other tetramers from the opposing membrane to form an adhesive lattice, like a molecular Velcro . The structure also suggests that P0 mediates adhesion through the direct interaction of apically directed tryptophan side chains with the opposing membrane [42], in addition to homo-philic protein-protein interaction. 

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. 

A key structural and mechanistic feature of lactate and malate dehydrogenases is the active site loop, residues 98-110 of the lactate enzyme, which was seen in the crystal structure to close over the reagents in the ternary complex.49,50 The loop has two functions it carries Arg-109, which helps to stabilize the transition state during hydride transfer and contacts around 101-103 are the main determinants of specificity. Tryptophan residues were placed in various parts of lactate dehydrogenase to monitor conformational changes during catalysis.54,59,60 Loop closure is the slowest of the motions. 

Besides having a noncovalent association of subunits as in tryptophan synthase, some enzymes are double-headed, in that they contain two distinct activities in a single polypeptide chain. A good example of this is the indole 3-glycerol phosphate-synthase-phosphoribosyl anthranilate isomerase bifunc-tional enzyme from the tryptophan operon of E. coli. The crystal structure of the complex has been solved at 2.0 A resolution.39 The two enzymes have been separated by genetic manipulation.40 The activity of the two separate monomeric monofunctional constituents is the same as in the covalent complex so there is no catalytic advantage of having the proteins fused. 

An interesting question is whether or not component selection occurs in the course of the self-assembly if a mixture is used, in particular in the case of chiral compounds. Thus, the assembly of a bis-L-tryptophan TAP derivative by di-w-butyl-B A was studied both as the optically pure LL compound and as a racemic mixture with the DD enantiomer [9.169]. The crystal structure of the latter showed... 

The revised structure for clavicipitic acid, suggested earlier by King etal.,44a has been confirmed, and the stereochemistry elucidated, by X-ray crystal-structure analysis.446 The major component of the naturally occurring mixture that constitutes clavicipitic acid was obtained pure by t.l.c. on silica gel, and proves to have the (55,10/ ) stereochemistry depicted in (53). The minor component of the mixture is presumably the (55,105)-diastereoisomer. It should be noted that, at present, the absolute configuration of clavicipitic acid rests only on its biogenetic derivation from L-tryptophan.446... 

Fig. 4. Computer graphics of the domain interface building the channel to the active center in PDC. The thiazolium ring of ThDP is visible at the bottom of the channel. A tryptophane residue (blue) has been engineered into the crystal structure of PDCS.u. by means of computer graphics. The picture was generated by J. Grotzinger using the program GRASP [181]...

Is and PBPRP1 may then represent an OBP-1 type of protein defined by key residues that may underlie specific functions. The ABPX/PBPRP-specific amino acid residues arginine at position 16, lysine at position 47, proline at position 76, threonine at position 92 are replaced respectively by leucine, glycine, lysine and lysine residues that are conserved in the different types of binding protein from B. mori (Krieger et al., 1993 Picimbon, 2001). These replacements may be relevant to support the function of ABPX. Based on the crystal structure of the bombykol-PBP complex, the tryptophane at position 101 and the valine 105 have been shown to contact the molecule of Bombykol (Sandler et al., 2000). These are replaced by two threonine residues characteristic of OBP-1. Therefore, the threonine residues characteristic of OBP Is may be of crucial importance for the binding specificities of these proteins. 

The potential for transition metal complexes to provide new reactivity patterns continues to be explored by the preparation of complexes and the study of their reactivity patterns. The aminoalkyl substituents of gramine, tryptamine and methyl tryptophanate promoted metalation at C2 of the indole ring by Pt(DMSO)2Cl2. The crystal structure of the gramine product was determined. 

Schematic views based on the crystal structure of the tryptophan synthase aifii complex (see Chapter for details).

The three-dimensional structure of the tryptophan synthase 02)82 complex from S. typhimurium reveals that the four polypeptide subunits are arranged in an extended a/8/Jo order forming a complex 150 A long.7 A schematic view of a single a/ ft pair based on the crystal structure is shown in the color plate . The 02)82 complex catalyzes the synthesis of L-tryptophan from indole-3-glycerol phosphate and L-serine, termed the a)3 reaction (Fig. 7.1). The a and )3 subunits can be separated and shown to catalyze two distinct reactions, termed the a and / reactions, respectively (Fig. 7.1). The rates of the a and / reactions are greatly increased when catalyzed by the 02)82 complex. Although the o)3 reaction is formally the sum of the a and )3 reactions, indole does not appear as a free intermediate in solution in this reaction.17-21 This result indicates that indole is a... 

The active sites of the a and /3 subunits are separated by 25-30 A and are connected by a tunnel of sufficient size to permit direct diffusion of indole between the heterologous active sites (Fig. 7.1).7) Fig. 7.1 shows our current picture of the mechanism of the a/3 reaction based on the crystal structure. The indole intermediate [IND] in Fig. 7.1, which is produced by cleavage of indole-3-glycerol phosphate at the a site, diffuses through an intramolecular tunnel to the / site where it undergoes a pyridoxal phosphate-dependent /3-replacement reaction with L-serine to form L-tryptophan. The catalytic mechanism of this reaction is described further in Section 7.7. 

Figure 35. Global mapping of surface hydration dynamics of apoMb. Shown is the X-ray crystal structure of sperm whale myoglobin (PDB ID 1MBD) in the holo form with eight helices A—H. In apo form, parts of the structure are melted and they are shown in transparent gray. The 16 balls indicate positions of mutation with tryptophan one at a time.

Fig. 3.6 Solvent access surfaces (colors represent electrostatic potentials) showing the exposed tryptophan residue (as yellow van der Waals spheres) involved in oxidation of lignin and other high redox-potential substrates by VP (a) and LiP (b). Lignin can be directly oxidized by VP at the tryptophan radical, while LiP requires the simultaneous presence of VA (synthesized by the fungus) acting as an enzyme-bound mediator [74]. Based on VP and LiP crystal structures (PDB 2BOQ and 1LLP, respectively)...

Choinowski T, Blodig W, Winterhalter K et al (1999) The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxyl group on the Cb of tryptophan 171 A novel radical site formed during redox cycle. J Mol Biol 286 809-827... 

---