Domain sequence

Domain Sequence of a polypeptide chain that can independently fold into a stable three-dimensional structure... 

Domain, sequence of amino acids in a protein that can be identified as controlling a specific function, that is, recognition of ligands. 

Fell JW, Boekhout T, Fonseca A et al (2000) Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int J Syst Evol Microbiol 50 1351-1371... 

Systematic cloning strategies based on the conserved motor domain sequences have identified a remarkable number of KRPs expressed in brain. Members of several KRP families expressed in brain have been implicated in forms of MBO transport. Kinesin-2 family members have been implicated in assembly and maintenance of cilia and... 

Fig. 4. Multiple sequence alignment of six distinct SH2 domain sequences. The SH2 domain notifiers are given on the left, the bottom line represents the consensus sequence as analyzed from the alignment. Highly conserved sequence positions are marked with capital letters. The sequential position of the major secondary structure elements (helices and sheets) are indicated by boxes...

Experience gained from protein structure determination in the past 30 years demonstrates that domains possessing similar sequences also possess similar folds, leading to the inference that such domains are members of homologous families (Doolittle, 1995 Henikoff etal., 1997). Some homologous domain sequences have diverged considerably beyond the level at which homology can be reliably predicted. However,... 

Another important aspect of structure prediction using PSSMs is the careful determination of the boundaries of distinct domains whose sequences are used as starting points to construct PSSMs. In iterative database searches, this is critical to avoid inclusion of more than one domain, which results in explosion of an iterative search instead of convergence. Using well-defined domain sequences is particularly important in the analysis of small binding domains that frequently are overlooked if combined with larger, usually enzymatic domains. 

Sigalas, I., Calvert, A. H., Anderson, J. J., Neal, D. E., and Lunec, J. (1996). Alternatively spliced mdm2 transcript with loss of p53 binding domain sequences transforming ability and frequent detection in human cancer. Nat. Med. 8, 912-917. 

The catalytic domain sequences do not seem to be strongly, or at least solely influenced by phylogeny. For example, we see in Family 1 the presence of both bacterial and fungal cellulase sequences. This family has a different relationship between its members than do Families 4 and 5, which are comprised of members of a single species. However, we do notice that cellulase sequences from a particular organism can be distributed into several different families. 

Enzyme amino acids domain sequence analysis performed... 

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,... 

SPECIFICITY DOMAIN SEQUENCE GAU PKTKR8PLTRAHLTEVESR LACS PQVVRTP LTRAHLTEMEQR PPR1 DPATGKOVPRCVVFF LEOR... 

Chatterjee TK, Fisher RA (2000) Cytoplasmic, nuclear, and golgi localization of RGS proteins. Evidence for N-terminal and RGS domain sequences as intracellular targeting motifs. J Biol Chem 275 24013-24021 Chatterjee TK, Fisher RA (2000) Novel alternative splicing and nuclear localization of human RGS 12 gene products. J Biol Chem 275 29660-29671... 

BOX 4.5. MODULATION OF THE CLEARANCE OF THERAPEUTIC PROTEINS BY ADDITION OF Fc DOMAIN SEQUENCES... 

As can be seen from the equation above, there is frequency domain subsampling. As a result, the analysis/synthesis system does critical sampling of the input signal, that is the number of time/frequency components for transform block is equal to the update length of the input time domain sequence. 

D-domain, which contains up to 30 cysteines and up to 400 amino acid residues, shows significant sequence identity with the other D-domains, especially the cysteine, glycine, and proline residues. Further analysis of the D-domain sequences has defined a potential domain, known as the trypsin inhibitor-like cysteine-rich domain (TIL) within each D-domain sequence (Lang et al. 2004). The NH2-terminal D-domains are involved in formation of mucin disulfide-linked oligomers/multimers (Perez-Vilar and Hill 1999 Perez-Vilar and Mabolo 2007 see Section 2.3.2). 

The pleckstrin-homology domain is named after pleckstrin, where it was found first (pleckstrin is a major platelet protein which is a substrate of protein kinase Pleckstrin and brain spectrin contain two domains, 2 about 120 residues each, with similar sequences in their amino- and carboxy-terminal parts. To date, at least 90 such PH-domain sequences have been described in proteins with very diverse functions, such as spectrin,43 cytosolic protein kinases, phospholipase C isoforms (PLC-P, -y, and the GTPase dynamin,44.45 guanine nucleotide exchange factors for monomeric GTP-bind-ing proteins, the GTPase-acdvating protein for Ras, the Ras-GAP, and cytoskeletal and several other proteins. 

Reproduced from Reference 17 with permission from the Royal Society of Chemistry. Unnecessary domain (sequence is indistinguishable from active Mon DH domains). The AT of module 5 should incorporate an ethylmalonate extender unit, and it contains a signature sequence very close to the propionate sequence. 

---