Active site identification

Shyue, S.K., K.H. Ruan, L.H. Wang, and K.K. Wu (1997). Prostacyclin synthase active sites. Identification by molecular modeling-guided site-directed mutagenesis. J. Biol. Chem. 272, 3657-3662. 

Zambelli T, Wintterlin J and ErtI G 1996 Identification of the active sites of a surface-catalyzed reaction Soienoe 273 1688-90... 

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

Definitive identification of lysine as the modified active-site residue has come from radioisotope-labeling studies. NaBH4 reduction of the aldolase Schiff base intermediate formed from C-labeled dihydroxyacetone-P yields an enzyme covalently labeled with C. Acid hydrolysis of the inactivated enzyme liberates a novel C-labeled amino acid, N -dihydroxypropyl-L-lysine. This is the product anticipated from reduction of the Schiff base formed between a lysine residue and the C-labeled dihydroxy-acetone-P. (The phosphate group is lost during acid hydrolysis of the inactivated enzyme.) The use of C labeling in a case such as this facilitates the separation and identification of the telltale amino acid. 

Branchini, B. R., et al. (1997). Identification of a firefly luciferase active site peptide using a benzophenone-based photooxidation reagent. J. Biol. Cbem. 272 19359-19364. 

Probably all adenylyl cyclases are inhibited competitively by substrate analogs, which bind at the site and to the enzyme configuration with which cation-ATP binds (cf Fig. 4). One of the best competitive inhibitors is (3-L-2, 3 -dideoxy adenosine-5 -triphosphate ( 3-L-2, 3 -dd-5 -ATP Table 4) [4], which allowed the identification of the two metal sites within the catalytic active site (cf Fig. 4) [3]. This ligand has also been labeled with 32P in the (3-phosphate and is a useful ligand for reversible, binding displacement assays of adenylyl cyclases [4]. The two inhibitors, 2, 5 -dd-3 -ATP and 3-L-2, 3 -dd-5 -ATP, are comparably potent... 

The elucidation of the X-ray structure of chymotrypsin (Ref. 1) and in a later stage of subtilisin (Ref. 2) revealed an active site with three crucial groups (Fig. 7.1)-the active serine, a neighboring histidine, and a buried aspartic acid. These three residues are frequently called the catalytic triad, and are designated here as Aspc Hisc Serc (where c indicates a catalytic residue). The identification of the location of the active-site groups and intense biochemical studies led to several mechanistic proposals for the action of serine proteases (see, for example, Refs. 1 and 2). However, it appears that without some way of translating the structural information to reaction-potential surfaces it is hard to discriminate between different alternative mechanisms. Thus it is instructive to use the procedure introduced in previous chapters and to examine the feasibility of different... 

Lewis DFV, Eddershaw PJ, Goldfarb PS, Tarbit MH. Molecular modelling of CYP3A4 from an alignment with CYP102 identification of key interactions between putative active site residues and CYP3A- specific chemicals. Xenobiotica 1996 10 1067-86. 

The power of the pooled GST fusion protein approach will increase as new biochemical reagents and assays become available. The development of chemical probes for biological processes, termed chemical biology, is a rapidly advancing field. For example, the chemical synthesis of an active site directed probe for identification of members of the serine hydrolase enzyme family has recently been described (Liu et al., 1999). The activity of the probe is based on the potent and irreversible inhibition of serine hydrolases by fluorophosphate (FP) derivatives such as diisopropyl fluorophosphate. The probe consists of a biotinylated long-chain fluorophosphonate, called FP-biotin (Liu et al., 1999). The FP-biotin was tested on crude tissue extracts from various organs of the rat. These experiments showed that the reagent can react with numerous serine hydrolases in crude extracts and can detect enzymes at subnanomolar... 

Abstract A review is provided on the contribution of modern surface-science studies to the understanding of the kinetics of DeNOx catalytic processes. A brief overview of the knowledge available on the adsorption of the nitrogen oxide reactants, with specific emphasis on NO, is provided first. A presentation of the measurements of NO, reduction kinetics carried out on well-characterized model system and on their implications on practical catalytic processes follows. Focus is placed on isothermal measurements using either molecular beams or atmospheric pressure environments. That discussion is then complemented with a review of the published research on the identification of the key reaction intermediates and on the determination of the nature of the active sites under realistic conditions. The link between surface-science studies and molecular computational modeling such as DFT calculations, and, more generally, the relevance of the studies performed under ultra-high vacuum to more realistic conditions, is also discussed. 

Chen JM, Rawlings ND, Stevens RA, Barrett AJ 1998 Identification of the active site of legumain links it to caspases, clostripain and gingipains in a new clan of cysteine endopeptidases. FEBS Lett 441 361-365... 

Hasslacher, M., Schall, M., Hayn, M. et al. (1996) Molecular cloning of the full-length cDNA of (5)-hydroxynitrile lyase from Hevea brasiliensis. Functional expression in Escherichia coli and Saccharomyces cerevisiae and identification of an active site residue. The Journal of Biological Chemistry, 271, 5884-5891. 

Activity-based protein profiling (ABPP) is a chemical proteomic strategy in which active-site-directed covalent probes are used to profile the functional states of enzymes in complex proteomes. Activity-based probes (ABPs) can distinguish active enzymes from their inactive zymogens or inhibitor-bound forms. They contain a reactive group intended to modify enzyme active sites covalently and a reporter group (typically rhodamine or biotin) that assists in detection and identification of protein targets. 

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