Protein Taxonomy

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

The fact that the folds can be classified into distinct stmctural classes (Levitt and Chothia, 1976 Brandon and Tooze, 1999) containing a number of related but variant stmctural subclasses (Richardson, 1981 Orengo et al., 1997) provided further evidence for their essentially natural status (see Figure 13.1). Levitt and Chothia (1976) derived one of the first structural protein taxonomies, dividing the folds into three main groups ot folds, (3 folds, and oc/(3 folds. In ot structures, the core is built up exclusively of ot helices in the (3 stmctures, the core is made up of antiparallel (3 sheets. The a/ 3 folds are made from combinations of (3-a-(3 motifs that form a predominantly (3 sheet core surrounded by helices (Brandon and Tooze, 1999). 

Levine, M., Muirhead, H., Stammers, D. K., and Stuart, D. L, 1978, Structure of pyruvate kinase and similarities with other enzymes Possible implications for protein taxonomy and evolution. Nature 271 626. 

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

CS Ring, DG Kneller, R Langndge, FE Cohen. Taxonomy and conformational analysis of loops m proteins. I Mol Biol 224 685-699, 1992. 

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

Richardson, J.S. The anatomy and taxonomy of protein stmcture. Adv. Prot. Chem. 34 167-339, 1981. Rossmann, M.G., Argos, P. Protein folding. Annu. Rev. 

Figure 5-1. Ramachandran plot of the main chain phi (< ) and psi (T) angles for approximately 1000 nonglycine residues in eight proteins whose structures were solved at high resolution. The dots represent allowable combinations and the spaces prohibited combinations of phi and psi angles. (Reproduced, with permission, from Richardson JS The anatomy and taxonomy of protein structures. Adv Protein Chem 1981 34 167.)...

Coelenterates and Echinoderms. Coelenterate and echinoderm toxins range from small molecular weight amines, to sterols, to large complex carbohydrate chains, to proteins of over 100,000 daltons. Molecular size sometimes reflects taxonomy, e.g., sea anemones (Actiniaria) all possess toxic polypeptides varying in size from 3,000 to 10,000 daltons while jellyfish contain toxic proteins (ca. 100,000 daltons). Carotenoids have been isolated from Asterias species (starfish), Echinoidea (sea urchins), and Anthozoans such as Actiniaria (sea anemones) and the corals. These are sometimes complexed with sterols (J5). 

Toward a Taxonomy of the Denatured State Small Angle Scattering Studies of Unfolded Proteins by Millett et al. assesses denatured states induced by heat, cold, and solvent for evidence of residual structure, while Insights into the Structure and Dynamics of Unfolded Proteins from NMR by Dyson and Wright describes their extensive investigations of residual structure in the unfolded state. 

TOWARD A TAXONOMY OF THE DENATURED STATE SMALL ANGLE SCATTERING STUDIES OF UNFOLDED PROTEINS... 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

The vast accumulation of information about protein structures provides a fresh opportunity to do descriptive natural history, as though we had been presented with the tropical jungles of a totally new planet. It is in the spirit of this new natural history that we will attempt to investigate the anatomy and taxonomy of protein structures. 

The biochemistry and taxonomy of cereals is relevant to their potential differential toxicity. The proteins in the cereal grains known as "gluten activate celiac disease. Gluten is a complex mixture of hundreds of related but distinct proteins. The grains considered capable of producing adverse effects in individuals with celiac disease include different species of wheat (e.g., durum, spelt, kamut), barley, rye, and their cross-bred hybrids (e.g., triticale, which is a cross between wheat and rye) (Ciclitira et ah, 2005 Cornell et ah, 2002 Dewar et ah, 2006 Howdle, 2006 Koning, 2008 Lester, 2008 Moron et ah, 2008 Thompson, 2000, 2001 Troncone et al., 2008a Vader et ah, 2003 Wieser and Koehler, 2008). 

In addition to their varied biological roles, non-heme iron proteins contain a magnificent assortment of iron sites having a multitude of chemical and structural properties. Indeed, the catalog of iron centers is a bit like the taxonomy of insects—a seemingly limitless variation of a few structural themes, yet each new form sufficiently different to define a new species. It is beyond the scope of any review of non-heme iron proteins to be inclusive, and there are excellent recent reviews which detail selected topics. Rather, it is our intention to provide in one chapter an overview of the major classes with an emphasis on proteins for which a crystal structure is available. This review begins with a survey of the types of protein iron structures and a discussion of some methods and problems associated with establishing the iron center type. This should provide an introduction to readers less familiar with the area. Sections II to IV include the current status and recent developments for a limited number of proteins from the major iron classes. These have been chosen in the subjective vein of a limited review the omission of a topic does not indicate its relative importance or interest, only the limitation of space. The purpose of this section is to emphasize the diversity of iron center structures and functions. 

---