Protein homologous families

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,... 

Mizuguchi, K., Deane, C. M., Blundell, T. L., and Overington, J. P. (1998) HOMSTRAD a database of protein structure alignments for homologous families. 

Deletion of the regulatory nirQ gene results simultaneously in a loss of the ability to reduce both nitrite and NO in P. stutzeri (Braun and Zumft, 1992). Nitrite reductase is synthesized and is active in vitro but nitric oxide reductase is synthesized in an inactive form. Although the exact function of the nirQ gene product is unknown, the gene encodes a protein homologous with the NtrC family of transcriptional activators (Zumft, 1993). 

As noted previously, three major classes of opioid receptors ( -, 5, and ) have been identified in various nervous system sites and in other tissues (Table 31-1). Each of the three major receptors has now been cloned. All are members of the G protein-coupled family of receptors and show significant amino acid sequence homologies. Multiple receptor subtypes have been proposed based on pharmacologic criteria, including 14, v-2, 1, 52 and k2, and k3. However, genes encoding... 

Nagasawa, S. Tokishita, S. Aiba, H. Mizuno, T. A novel sensor-regulator protein that belongs to the homologous family of signal-transduction proteins involved in adaptive responses in Escherichia coli. Mol. Microbiol., 6, 799-807 (1991)... 

The correctness of hits corresponding to families with known structural information is further verified by employing the protein fold recognition method PHYRE (Protein Homology/analogY Recognition Engine) version 0.2, which assesses the compatibility of a sequence to a three-dimensional structure (29). 

PTPS (6-Pyruvoyl Tetmhydropterin Synthase). 6-Pyruvoyl tetrahy-dropterin synthase catalyzes formation of tetrahydrobiopterin biosynthesis. Tetrahydrobiopterin is a cofactor for several important enzymes, such as aromatic amino acid hydroxylases and nitric oxide synthase (57). H. pylori protein HPAG1 0913 shares homology with members of the protein domain family PTPS. H. pylori protein shares poor sequence identity of 14% with the PTPS profile at an E-value of 10 10 and covers about 95% of the length of the profile. Fold recognition results also confirm the relationship between H. pylori protein and the PTPS protein domain family. A fold recognition algorithm ensures fitness of the H. pylori protein sequence on the three-dimensional structure of PTPS from... 

Proteins homologous to the cytosolic cyclophilins from vertebrates or the corresponding genes are found virtually in every organism and in every subcellular compartment. All members of this family that could be obtained in purified form had a high prolyl isomerase activity and were inhibited by CsA, albeit with different effectiveness. Notably, the affinity... 

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