Catalytic residue

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

Matsuura, Y., et al. Structure and possible catalytic residues of taka-amylase A. /. Bioehem. 95 ... 

This idea also helps to explain some of the mystery surrounding the enormous catalytic power of enzymes In enzyme catalysis, precise orientation of catalytic residues comprising the active site is necessary for the reaction to occur substrate binding induces this precise orientation by the changes it causes in the protein s conformation. 

An enzyme in which the single catalytic residue is at the N-terminus of the protein. Many Ntn-hydrolases are synthesized as precursors and autoactivate the precursors are therefore peptidases, even if the mature enzyme has no further proteolytic activity. Three of the beta subunits of the proteasome are Ntn-hydrolases. 

Hen egg-white lysozyme catalyzes the hydrolysis of various oligosaccharides, especially those of bacterial cell walls. The elucidation of the X-ray structure of this enzyme by David Phillips and co-workers (Ref. 1) provided the first glimpse of the structure of an enzyme-active site. The determination of the structure of this enzyme with trisaccharide competitive inhibitors and biochemical studies led to a detailed model for lysozyme and its hexa N-acetyl glucoseamine (hexa-NAG) substrate (Fig. 6.1). These studies identified the C-O bond between the D and E residues of the substrate as the bond which is being specifically cleaved by the enzyme and located the residues Glu 37 and Asp 52 as the major catalytic residues. The initial structural studies led to various proposals of how catalysis might take place. Here we consider these proposals and show how to examine their validity by computer modeling approaches. 

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... 

One of the most direct questions to ask in the perspective of enzyme design is whether an already existing protein with a binding pocket might be turned into a new catalyst by introducing catalytic residues directly, rather than by the elaborated TSA mimicry approach used for catalytic antibodies, hoping to create a new biocatalyst that could harness both the activity and the selectivity, in particular stereoselectivity, that is possible with enzymes. 

Figure 7-5. Two-dimensional representation of Koshland s induced fit model of the active site of a lyase. Binding of the substrate A—B induces conformational changes In the enzyme that aligns catalytic residues which participate in catalysis and strains the bond between A and B, facilitating its cleavage.

Fischer, F., and Fetzner, S., Site-Directed Mutagenesis of Potential Catalytic Residues in lh-3-Hydroxy-4-Oxoquinoline 2, 4-Dioxygenase, and Hypothesis on the Catalytic Mechanism of 2, 4-Dioxygenolytic Ring Cleavage. FEMS Microbiol Lett, 2000. 190 pp. 21-27. 

Boesen, T., Mohammad, S. S., Pavitt, G. D., and Andersen, G. R. (2004). Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue. /. Biol. Chem. 279, 10584—10592. 

L. K. Ozimek, S. A. van Hijum, G. A. van Koningsveld, M. J. van Der Maarel, G. H. van Geel-Schutten, and L. Dijkhuizen, Site-directed mutagenesis study of the three catalytic residues of the fructosyltransferases of Lactobacillus reuteri 121, FEBS Lett., 560 (2004) 131-133. 

FIGURE 11-7 Gene structure of AChE. Alternative cap sites in the 5 end of the gene allow for alternative promoter usage in different tissues. Skeletal-muscle-specific regulation is controlled by the intron region between Exons 1 and 2. Exons 2, 3 and 4 encode an invariant core of the molecule that contains the essential catalytic residues. Just prior to the stop codon, three splicing alternatives are evident 1, a continuation of exon 4 2, the 4-5 splice and 3, the 4-6 splice. The catalytic subunits produced differ only in their carboxy-termini and are shown in the lower panel. (Modified with permission from reference [24].)... 

All GTP binding proteins in signal transduction share a common structural element - the Ras-like domain which is responsible for the specific complexation of guanosine diphosphate and -triphosphate and which contains catalytic residues that promote GTP-hydrolysis. 

Each CHS monomer consists of two structural domains (Fig. 12.5, left). The upper domain exhibits the a-p-a-p-a pseudo-symmetric motif observed in fatty acid P-ketoacyl synthases (KASs) (Fig. 12.5, right).20 Both CHS and KAS use a cysteine as a nucleophile in the condensation reaction, and shuttle reaction intermediates via CoA thioester-linked molecules or ACPs, respectively. The conserved architecture of the upper domain maintains the three-dimensional position of the catalytic residues of each enzyme Cysl64, His303, and Asn336 in CHS correspond to a Cys, His, and His in KAS I and II. 

Figure 12.5 A. Comparison of the CHS monomer (left) and P-ketoacyl synthase monomer (right). The structurally conserved secondary structure of each monomer s upper domain is colored in blue (a-helix) and gold (P-strand). Portions of each protein monomer forming the dimer interface are colored purple. The side-chains of the catalytic residues of CHS (Cysl64, His303, Asn336) and P-ketoacyl synthase (Cysl63, His303, His340) are shown. B. Sequence conservation of the catalytic residues of CHS, 2-PS, p-ketoacyl synthase (FAS II), and the ketosynthase modules of 6-deoxyerythronolide B synthase (DEBS), actinorhodin synthase (ActI) and tetracenomycin synthase (TcmK). The catalytic residues are in red.

Figure 12.6 Starter molecule engineering. A. Reaction catalyzed by ACS. B. Thin layer chromatography screening for enzymatic activity with different starter molecules. C. Views illustrate the active site of the F215S mutant (right), wild-type CHS with N-methylanthraniloyl-CoA (center), and wild-type CHS with p-coumaroyl-CoA (left) modeled at the active site entrances. The catalytic residues, Cys 164, His 303, and Asn 336, and Phe 265 are shown. In wild-type CHS, N-methylanthraniloyl-CoA clashes with Phe 215 to prevent the CoA thioester from adopting the conformation depicted in (A). The wild-type - p-coumaroyl-CoA model emphasizes the ability of the propanoid linker to extend the phenolic ring deeper into the active site cavity.

The partitioning of the system in a QM/MM calculation is simpler if it is possible to avoid separating covalently bonded atoms at the border between the QM and the MM regions. An example is the enzyme chorismate mutase [39] for which the QM region could include only the substrate, because the enzyme does not chemically catalyze this pericyclic reaction. In studies of enzyme mechanisms, however, this situation is exceptional, and usually it will be essential, or desirable, to include parts of the protein (for example catalytic residues) in the QM region of a QM/MM calculation, i.e. the boundary between the QM and MM regions will separate covalently bonded atoms (Fig. 6.1). 

Skeletal copper is best made from the CuA12 intermetallic compound which has very close to 50 wt% aluminum in the alloy and gives an active and selective catalyst [27-29], Skeletal nickel is also best made from an alloy of about 50 wt% aluminum [25] however, in this case, the alloy consists of more than one intermetallic phase, the combination of which provides the best activity while maintaining adequate strength in the catalytic residue. The most active skeletal cobalt catalysts are made from an alloy of about 60-65 wt% aluminum, which consists of two intermetallic phases, Co2A19 + Co4A113 [30],... 

Clan Types of families Catalytic residue(s) 3D Structure... 

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