Enzyme domain structure

The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Antiparallel beta (P) structures comprise the second large group of protein domain structures. Functionally, this group is the most diverse it includes enzymes, transport proteins, antibodies, cell surface proteins, and virus coat proteins. The cores of these domains are built up by p strands that can vary in number from four or five to over ten. The P strands are arranged in a predominantly antiparallel fashion and usually in such a way that they form two P sheets that are joined together and packed against each other. 

The two isozymes are both homodimers, composed of approximately 600 amino acids and possess approximately 60% homology. The three-dimensional structures of COX-1 and COX-2 are very similar. Each one consists of three independent units an epidermal growth factor-like domain, a membrane-binding section and an enzymic domain. The catalytic sites and the residues immediately adjacent are identical but for two small but crucial variations that result in an increase in the volume of the COX-2-active site, enabling it to accept inhibitor-molecules larger than those that could be accommodated in the COX-1 molecule. 

Figure 5-6. Examples of tertiary structure of proteins. Top The enzyme triose phosphate isomerase. Note the elegant and symmetrical arrangement of alternating p sheets and a helices. (Courtesy of J Richardson.) Bottom Two-domain structure of the subunit of a homodimeric enzyme, a bacterial class II HMG-CoA reductase. As indicated by the numbered residues, the single polypeptide begins in the large domain, enters the small domain, and ends in the large domain. (Courtesy ofC Lawrence, V Rod well, and C Stauffacher, Purdue University.)...

The published filarial chitinases show a distinct modular domain structure (Fig. 10.3). The first 17-22 amino acids serve as a cleavable signal sequence, indicating that the enzymes are secreted or are components of the outer membrane. The catalytic domain, essential for the degradation of... 

It is worth mentioning that membrane-bound forms of GC, which can be considered signal transducing enzymes , are structurally homologous to other signal transducing enzymes, such as certain protein tyrosine kinases and phosphatases, which also possess receptor moieties in their extracellular (amino terminus) domain and enzyme catalytic activity in their intracellular domain (see Ch. 24). Activation of many of these receptors occurs upon ligand-induced dimerization of the receptors, and a similar... 

Methylenetetrahydrofolate reductase (MTHFR) catalyzes the NAD(P)H-dependent reduction of 5,10-methylenetetrahydrofolate (CH2-THF) to 5-methyltetrahydrofolate (CH3-THF). CH3-THF then serves as a methyl donor for the synthesis of methionine. The MTHFR proteins and genes from mammalian liver and E. coli have been characterized,12"15 and MTHFR genes have been identified in S. cerevisiae16 and other organisms. The MTHFR of E. coli (MetF) is a homotetramer of 33-kDa subunits that prefers NADH as reductant,12 whereas mammalian MTHFRs are homodimers of 77-kDa subunits that prefer NADPH and are allosterically inhibited by AdoMet.13,14 Mammalian MTHFRs have a two-domain structure the amino-terminal domain shows 30% sequence identity to E. coli MetF, and is catalytic the carboxyterminal domain has been implicated in AdoMet-mediated inhibition of enzyme activity.13,14... 

Ghosh, D. K., Salerno, J. C., Nitric oxide synthases domain structure and alignment in enzyme function and control. Front. Biosci. 8 (2003),... 

Description of domain structure of a protein Description of enzyme regulatory mechanism General description of function (s) of a protein Description of compound (s) that stimulate synthesis of a protein... 

Its length can vary from 30 to more than 100 residues. It is rich in serine and threonine but deficient in acidic residues. It is not clear whether it has the three-domain structure like the signal peptide (von Heijne et al., 1989). Recently, a chloroplast-processing enzyme was identified as the general stromal processing peptidase (Richter and Lamppa, 1998). 

This class of receptors transmits signals carried by hormones and growth factors. The structure consists of an extracellular domain for binding ligands and a cytoplasmic enzyme domain. The function of kinases is to enable phosphorylation. Phosphorylation regulates most aspects of cell life. 

Figure 10 Schematic illustration of the posttranslational enzymes and related proteins. P4H a subunits have three isoforms. Each has three domains. The substrate-binding domain is in the middle. The catalytic domain is at the C-terminal end. Lysyl hydroxylase-3 (LH3) has two different catalytic activities. The N-terminal domain has the glucosyltransferase activity and the C-terminal domain has the hydroxylase activity. LH1 and LH2 also have similar domain structures but the glucosyltransferase activities are not detected in vitro.

Structural analysis of several non-NRPS adenyiation domains has provided significant insight into the basis for the multistep chemistry of NRPS A domains. Of note, the X-ray structures of 4-chlorobenzoate-CoA ligase bound to reaction intermediates showed two dramatically different orientations between the large and small domains. The enzyme bound to a substrate analogue was in a similar conformation as the described NRPS A-domain structures. In contrast, the structure of the enzyme bound to a product analogue revealed that... 

The analysis presented above for the effect of ceUobiose on CBH I thermal stability must be considered preliminary, in that equation 3, and therefore also equation 4, which is derived from equation 3, apply strictly only to single-transition processes. Equation 4 does, however, serve weU to illustrate the general type of peak-displacement being proposed here. Exact numerical appUcation of such an equation would require accurate estimates, not presently avaUable, for such quantities as the K. values for native CBH I and ceUobiose at pH values far remov from the activity optimum, and/or at temperatures at which the native enzyme, in the absence of the inhibitor, does not exist in measurable proportions. QuaUtatively, however, we beUeve that the analysis presented above can serve as a useful conceptual basis, or springboard, for further investigations of catalytic-domain structure and function. 

Comparative evaluation of the domain structure and phylogenetic reconstruction of the sequences of [FeFe] hydrogenases still leave the challenging question of the origin and history of this enzyme in eukaryotic organisms wide open (Meyer 2007). 

All NOS proteins possess a bi-domain structure, and dimerization to homodimers (> 260 kDa each), is required for enzyme activity (see Tablel). 

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