Enzymes structure prediction

The term "structural genomics" is used to describe how the primary sequence of amino acids in a protein relates to the function of that protein. Currently, the core of structural genomics is protein structure determination, primarily by X-ray crystallography, and the design of computer programs to predict protein fold structures for new proteins based on their amino acid sequences and structural principles derived from those proteins whose 3-dimensional structures have been determined. Plant natural product pathways are a unique source of information for the structural biologist in view of the almost endless catalytic diversity encountered in the various pathway enzymes, but based on a finite number of reaction types. Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the... 

What is the exact influence of water and organic molecules on the enzyme structure Could its effects on properties such as selectivity, affinity, binding constants, and catalytic constants be predictable by controlling the hydration/solvation state ... 

Protein design by site-directed mutagenesis on pyruvate decarboxylase became possible after the 3D-structure of the enzyme from Saccharomyces uvarum had become available [35], Based on sequence comparison and secondary structure prediction, the 3D-structure of the yeast enzyme served as a model for PDCZ.m. [163], The point mutations which have been introduced into the two enzymes (Tables 4 and 5) concern catalytically important residues as well as significant side-chain interactions at the domain interface of the dimer. Besides, site-directed mutagenesis offered a powerful tool to improve the car-boligase reaction of PDCZ.m. with respect to the synthesis of (P)-PAC [163,164,170]. 

Hundreds of mutant P-type ATPases have been generated in an effort to understand the catalytic mechanism and regulation of these enzymes. Functional analysis of these mutants has established the roles of particular domains and amino acid residues in the overall catalysis of cation translocation and allowed structure prediction (MacLennan etal., 1997) (Figs. 1 and 2). Recently the 3-D or crystal structures of Ca +, H+, and Na+/K+ P-type ATPases have been resolved, and they confirmed findings... 

The earliest observation that implied evolutionary links between all lipases was that of the consensus pentapeptide G-X-S-X-G, subsequently shown to contain the nucleophilic serine. The apparent similarity of this sequence to that found around the active serine in the chy-motrypsin and subtilisin families of serine proteinases prompted a number of authors to infer an evolutionary relationship between the three families. Further evidence in support of such a link came from secondary structure prediction studies indicating that the nucleophilic serine in a lipase is most likely within a /3 turn, structurally reminiscent of proteinases (Reddy et ai, 1986). In fact, one of the commonly used phrases found in introductions to many papers dealing directly or indirectly with lipases refers to the consensus G-X-S-X-G pentapeptide found in the active site of all serine proteinases and esterases. We now know that the implication that homology and/or structural similarities exist between the enzymes belonging to these diverse groups is incorrect. The matter has been dealt with in the literature (Derewenda and Derewenda, 1991 Liao et ai, 1992), but it seems appropriate to review some of the conclusions. 

The membrane-bound cytochrome 655s (Bacillus subtilis) contains, according to secondary structure predictions, five transmembrane helices. It functions to anchor two other subunits of the succinate quinone oxidoreductase complex (complex II, E.C. 1.3.5.1) in the cytoplasmic membrane (68). The 1.3-2.0 hemes per covalently bound flavin have been found with the isolated enzyme. The amino acid residues that bind the heme between the a-helices are likely bis(histidine). The EPR and NIR MCD spectra are consistent with this because the EPR spectra show a g value of 3.4 with a HALS lineshape, and the MCD spectra show a low-spin CT band at 1600 nm with Ae of 380 M cm at 4.2 K and 5 T (69). This appears to be another example of a bis(histi-dine)-coordinated heme with near perpendicular alignment of the ligands. 

---