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Protein structural similarities predicted by a sequence‐structure compatibility method
Author(s) -
Matsuo Yo,
Nishikawa Ken
Publication year - 1994
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560031118
Subject(s) - biochemistry , structural similarity , biology , peptide sequence , threonine , sequence motif , protein structure , structural motif , threading (protein sequence) , serine , enzyme , dna , gene
A method for protein structure prediction has been developed, which evaluates the compatibility of an amino acid sequence with known 3‐dimensional structures and identifies the most likely structure. The method was applied to a large number of sequences in a database, and the structures of the following proteins were predicted: (1) shikimate kinase (SKase), (2) the hydrophilic subunit of mannose permease (IIAB Man ), (3) rat tyrosine aminotransferase (Tyr AT), and (4) threonine dehydratase (TDH). The functional and evolutionary implications of the predictions are discussed. (1) The structural similarity between SKase and adenylate kinase was predicted. Alignment of their sequences reveals that the ATP‐binding type A sequence motif and 2 ATP‐binding arginine residues are conserved. The prediction suggests a similarity in their functional mechanisms as well as an evolutionary relationship. (2) The structural similarity between IIAB Man and galactose/glucose‐binding protein (GGBP) was predicted. The IIA and IIB domains are aligned with the N‐and C‐terminal domains of GGBP, respectively. The 2 phosphorylated residues, His 10 and His 175, of IIAB Man are threaded onto loops located in the substrate‐binding cleft of GGBP. The prediction accounts for the phosphoryl transfer from His 10 to His 175, and to the sugar substrate. (3) The structural similarity between rat Tyr AT and Escherichia coli aspartate AT was predicted, as well as (4) the structural similarity between TDH and the tryptophan synthase β subunit. Predictions (3) and (4) support the previous predictions based on observations of the functional similarities between the proteins.