Native crystallographic studies

From crystallographic studies, fast reaction kinetics and site-directed mutagenesis to produce mutant enzymes differing from the native enzyme in one or more specified residues, the mechanism in (46) has been proposed for the attack of water at the carbonyl carbon of benzoylglycylphenylalanine bound to carboxypeptidase (Christianson and Lipscomb, 1989). 

The Di Xia research group has completed X-ray crystallographic studies of cytochrome bci with a number of different inhibitors (PDB ISQB, ISQP, ISQQ, ISQV, ISQX). Crystals suitable for crystallography were obtained by co-crystallization of the inhibitor with the native enzyme. Data for two of the inhibitor-modified cytochrome bci complex (PDB ISQP and ISQX) are included in Table 7.6 and Table 7.7. Qne inhibitor-enzyme complex studied by... 

In 2003, the Di Xia group published an X-ray crystallographic study of substrate and inhibitor molecules at the Qo and Qi site. They intended to compare the structure of the native enzyme (PDB INTM) with the cytochrome bci complex having substrate or inhibitors in the Qo and/or Qi sites. The complex with substrate ubiquinone UQ2 (PDB INTZ) was discussed previously in this section. The complex with the inhibitor antimycin Ai (PDB INTK) will be discussed here. A fourth complex with the ubiquinone-model... 

Wu N, Pai EP (2004) Crystallographic Studies of Native and Mutant Orotidine 5 -Phosphate Decarboxylases. 238 23-42... 

X-Ray crystallographic studies of native human carbonic anhydrase II have been reported at 2.0 A resolution (Eriksson et al, 1986, 1988a). Important active-site residues include Thr-199, Thr-200, Glu-106, His-64, Trp-209, Val-121, Val-143, the zinc ion (liganded by His-94, His-96, and His-119), and the zinc-bound hydroxide ion. A schematic view of the active site is found in Fig. 22. The globular protein has a molecular... 

The UV spectra of these complexes are very similar to those found in tetrahedral complexes of Co11 known to have a somewhat distorted geometry, suggesting a similar geometry in the cobalt enzyme.1383 Tetrahedral mercaptide complexes of the type [Co(SPh)4]2- were also shown to have similar absorption characteristics to those of [(LADH)Co2Co2j. This work is in complete agreement with the X-ray crystallographic studies of the native LADH, already mentioned, which shows distorted tetrahedral coordination of both the catalytic and non-catalytic zinc atoms of the enzyme. 

Crystallographic studies of native cysteine proteinases and enzyme-inhibitor complexes have been used to interpret much or the kinetic data for cysteine protemsse-caUlyzed hydrolysis of amide bonds. Analysis of the crystal structures of papain [16]. caricain [38], actinidain [56], etc. shows that these structures are closely related. The active site of all these cysteine proteinases contains the Cys-25 sulfhydryl group in close proximity to the His-159 imidazole ring nitrogens, where the latter can abstract the sulfhydryl proton to facilitate attack on the substrate amide carbonyl group [17]. 

It was suggested, based on UV-visible and EPR spectroscopy, that the ribonucleotide reductase from Corynebac-terium ammoniagenes contains Mn rather than Fe in its native form. However, more recent crystallographic studies have shown that this protein is structurally identical to the native iron proteins and apparently does not contain a Mn active... 

In addition to the disallowed reflections in the electron diffraction patterns that placed the crystallographic models in question, new spectral evidence was developed pointing to the need for further refinement of structural models, particularly for native celluloses. The models derived from the crystallographic studies could not rationalize many features of the spectral data known to be quite sensitive to structural variations. 

The first indication that several conformations could be observed came from the comparison of the NMR solution and an earlier X-ray structure of the Oxytricha bimolecular quadruplex. The initial X-ray structure contained many of the features found in the solution structure but differed in the orientation of the thymine loops edge-loops were observed by X-ray as compared to diagonal-loops in the NMR structure. However, a recent analysis corrected this earlier crystallographic study and demonstrated that this quadruplex adopts a structure with two strands forming an antiparallel diagonal arrangement, indicating that the native structure is the same in solution and in the crystalline state. 

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