Conserved Residue Attributes

Only protein structures solved to resolution better than 3.0 A from the Protein Data Bank are considered. The 3D templates are generated with CORA (Conserved Residue Attributes) for recognition of structural relatives in each fold group (Orengo, 1999). The CATH Architectural descriptions that denote the arrangements of secondary structures are given in Table 12.2. 

Only protein structures solved to resolution better than 3.0 A from the Protein Data Bank are considered. The 3D templates are generated with Conserved Residue Attributes... 

Caspases are a family of evolutionary conserved cysteine proteases that cleave their substrates after an aspartic acid residue within a defined consensus sequence (Alnemri et al, 1996). They play a cracial role in the apoptotic program, as most of the characteristic features observed in apoptosis are attributable to their action (Eamshaw et al, 1999). They are... 

In a supplementary pathway, links between histone H3 Lys4 methylation and the upregulation of RNA synthesis have also been made. This discrete modification colocalizes with acetylated histone residues and is enriched in the transcriptionally active macronucleus of Tetrahymena [194]. Histone methylation at H3 Lys4 has been recently attributed to the novel HMT SET9, which contains the conserved SET catalytic domain, and noticeably lacks the juxtaposed pre- and post-SET... 

Suprafamilies a group of homologous enzymes that catalyze different overall reactions which do not share common mechanistic attributes and do not share a high level of sequence identity (< 20%) but are metabolically linked such as in successive reactions. Active-site residues may be conserved but perform different functions in family members.Tables 16.2 and 16.3 list known superfamilies and suprafamilies with some of their family members. 

Sequence patterns Protein sequence is not well conserved, because protein function is often attributed to only a small set of residues, such as the catalytic triad Serine-Histidine-Aspartate in serine protease enzymes. Special algorithms have been developed to find these patterns or motifs, of which the constituting parts are most often discontinuous parts of a protein sequence. 

As discussed previously (Section IV), residues 245-280 of bovine GDH display sequence homology with the residues comprising the coenzyme binding domain of the dehydrogenases of known three-dimensional structure and sequence. Moreover, the three residues to which a functional role has been attributed are all conserved in GDH and those residues, believed to lie facing the /3-pleated sheet regions, are either identical or functionally conserved in GDH when compared to other dehydrogenases. It seems likely, therefore, that residues 245-280 of bovine GDH comprise a portion of the adenylate subsite within the active site for coenzyme [subsite II in the Cross and Fisher model 309)]. 

The amino acid sequences of four avian insulins have been determined, namely domestic fowl, turkey, duck and goose. Those of domestic fowl and turkey are identical but differ from that of the duck and goose at three positions (Fig. 7.2). There are also differences in the size of the C-peptide, which is 28 residues in the domestic fowl and 26 in the duck. Another feature that is evident from the proinsulin sequence (Fig. 7.2) is that the C-peptide is less conserved than the A- and B-peptides. tW C-peptide simply acts as a link between the A- and B-peptides to enable the disulphide bridges to form. Domestic fowl insulin is more potent than bovine insulin in ellidting changes in metabolism in the domestic fowl. This has been attributed to the six differences in the amino acid sequences of the two proteins. 

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