Three-domain classification system

Table 3.3 Three domain system of classification (after Campbell et al, 1999).

SCOP, CATH, and DDD agree on most of their classifications, despite differences in the classification methods they have implemented, and in the rules of protein structure and taxonomy they are based on. Hadley and Jones were the first to publish a detailed comparison of the fold classifications produced by SCOP, CATH, and FSSP. They showed that the three classification systems tend to agree in most cases, and that the discrepancies and inconsistencies are accounted for by a small number of problems. Among these, the domain assignment plays a crucial role. As mentioned, the separation of proteins into domains is a difficult and often subjective process. Many... 

Peptidases have been classified by the MEROPS system since 1993 [2], which has been available viatheMEROPS database since 1996 [3]. The classification is based on sequence and structural similarities. Because peptidases are often multidomain proteins, only the domain directly involved in catalysis, and which beais the active site residues, is used in comparisons. This domain is known as the peptidase unit. Peptidases with statistically significant peptidase unit sequence similarities are included in the same family. To date 186 families of peptidase have been detected. Examples from 86 of these families are known in humans. A family is named from a letter representing the catalytic type ( A for aspartic, G for glutamic, M for metallo, C for cysteine, S for serine and T for threonine) plus a number. Examples of family names are shown in Table 1. There are 53 families of metallopeptidases (24 in human), 14 of aspartic peptidases (three of which are found in human), 62 of cysteine peptidases (19 in human), 42 of serine peptidases (17 in human), four of threonine peptidases (three in human), one of ghitamicpeptidases and nine families for which the catalytic type is unknown (one in human). It should be noted that within a family not all of the members will be peptidases. Usually non-peptidase homologues are a minority and can be easily detected because not all of the active site residues are conserved. 

The domains of inorganic supramolecularity are valuable also as a classification to accommodate substantial chemical diversity. While it is often true in inorganic systems that the peripheral domain P is heavily populated with organic substituents (jocularly dubbed the spinach ), such that the molecules look organic from the outside, in fact the intrigue of inorganic chemistry is that most elements can occur in any of the domains, and the supramolecular interactions and considerations can be much more variable than for conventional organic molecules. The three molecular domains may constitute very different proportions of the molecular volume. 

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