Protein domains classification

CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH—A hierarchic classification of protein domain structures. Stnrcture 5 1093-1108, 1997. 

In order to make as much data on the structure and its determination available in the databases, approaches for automated data harvesting are being developed. Structure classification schemes, as implemented for example in the SCOP, CATH, andFSSP databases, elucidate the relationship between protein folds and function and shed light on the evolution of protein domains. 

Selected entries from Methods in Enzymology [vol, page(s)] General Protein kinase classification, 200, 3 protein kinase catalytic domain sequence database identification of conserved features of primary structure and classification of family members,... 

The CATH protein domain database (http //www.biochem.ucl.ac.uk/bsm/cath) is a hierarchical classification of protein domain structures into evolutionary families and structural groupings depending on sequence and structure similarity (Pearl et al, 2000). The protein domains are classified according to four major levels. 

PALI (Phylogeny and Alignment of Homologous Protein Domains) Database. The PALI (v 2.6) database provides three-dimensional structure-based sequence alignments for homologous proteins of known three-dimensional structure (24-26). The protein families have been derived from the SCOP (Structural Classification of Proteins) database (27). There are 2,518 protein families, and using more than one sequence as reference, 37,986 profiles have been generated. 

The classification of the four subfamilies, stellacyanins, plantacyanins, uclacyanins, and early nodulins, is based (i) on their spectroscopic features, (ii) on precursor as well as mature protein domain organization. 

Figure 13.1. Structural classes of protein folds, showing how the folds can be classified into different structural classes. Top row the three basic fold classes a, containing only a helices a and p, containing a helices and p sheets and p, containing only p sheets. Middle row three different architectural subclasses of the a and p class triosephosphate isomerase (TIM) barrel, three-layer sandwich, and roll. Bottom row two different arrangements of the "three-layer sandwich . The spiral conformations are the a helices, and the broad arrows are the p sheets. (From Orengo, C. A., Michie, A. D., Jones, S. et al. [1997]. CATH - a hierarchic classification of protein domain structures [Figure 2]. Structure, 5, 1093-108. Copyright 1997, Elsevier Science. Reprinted with permission.)...

Orengo, C. A., Michie, A. D., Jones, S. et al. (1997). CATH - a hierarchic classification of protein domain structures. Structure. 5(8), 1093-108. See cathwww.biochem.ucl.ac.uk/latest/index.html. 

A comprehensive description of the databases and methods for domain, family, and pattern identification is available in chapter 2. Therefore, in this chapter, the discussion of the application of family and domain information to function assignment will be limited to Pfam, the virtual standard in protein domain/family classification, and to InterPro and CDD, two resources that integrate multiple domain databases. In addition, I discuss tools that can be used to scan those databases, namely HMMER,... 

M. Levitt and C. Chothia (81) constructed taxonomic classifications of protein structure and noted that a helix and (3 sheet structures within protein domains are organized in a limited number of ways. The four main subcategories are named a for a-helical proteins, 3 for proteins that are primarily composed of 3 sheets, a + 3 for proteins with both a helices and 3 sheets, and a/3 for those proteins that have alternating a-helix- and 3-sheet arrangements. 

As has been described in Sect. 5.3, the conservation patterns of enzymes are often indicative of the particular family they belong to and can be used for their classification. However, the iterative searches and multiple alignment methods used for their establishment require a certain bioinformatic infrastructure as well as some experience with these issues. If the goal of the analysis is not the detection of novel enzyme families, but rather the classification of a novel sequence into one of the already existing enzyme families, there are a number of protein domain and motif databases that will be useful in this respect[60 61. These databases do not store the sequences themselves but rather work with descriptors of protein families and protein domains. These descriptors can consist of the Profiles or Hidden Markov Models mentioned above, but other types are also being used. With a particular... 

Qrengo, C.A., et al. GATH—A hierarchic classification of protein domain structures. Structure 1997, 5(8), 1093-108. 

Many proteins share structural similarities due to the evolutionary process involving substitutions, insertions and deletions in amino add sequences. Consequently protein structures can be characterized according to their connnon substructures (supersecondary structures, e.g. motifs, domains). For proteins with conserved functions, the structural environments of critical active site residues are also conserved. In an attempt to better understand seqnence-structuie relationships and the underlying evolutionary processes that give rise to different fold famihes, a variety of structure classification schemes have been established. Analyses of the 3D structures archived in PDB generate various databases for the specification/search of characteristic substructures and protein structure classifications (Table 16.6). 

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