Determination of the base recognition positions of zinc fingers from sequence analysis
Autor: | Jacobs Gh |
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Rok vydání: | 1992 |
Předmět: |
Models
Molecular Stereochemistry Sequence analysis Molecular Sequence Data Molecular Conformation chemistry.chemical_element Sequence alignment Zinc Biology General Biochemistry Genetics and Molecular Biology Conserved sequence Amino Acid Sequence Molecular Biology Peptide sequence Conserved Sequence Histidine Genetics Zinc finger Binding Sites General Immunology and Microbiology General Neuroscience Zinc Fingers DNA Protein superfamily chemistry Sequence Alignment Research Article |
Zdroj: | The EMBO Journal. 11:4507-4517 |
ISSN: | 0261-4189 |
Popis: | The CC/HH zinc finger is a small independently folded DNA recognition motif found in many eukaryotic proteins, which ligates zinc through two cysteine and two histidine ligands. A database of 1340 zinc fingers from 221 proteins has been constructed and a program for analysis of aligned sequences written. This paper describes sequence analysis aimed at determining the amino acid positions that recognize the DNA bases, by comparing two types of sequence variation. Using the idea that long runs of adjacent zinc fingers have arisen from internal gene duplication, the conservation of each position of the finger within the runs was calculated. The conservation of each position of the finger between homologous proteins from different species was also noted. A correlation of the two types of conservation showed clusters of related amino acids. One cluster of three positions was found to be especially variable within long runs, but highly conserved between corresponding fingers of homologous proteins; these positions are predicted to be the base contact positions. They match the amino acid positions that contact the bases in the co-crystal structure determined by Pavletich and Pabo [Science, 240, 809-817 (1991)]. An adjacent cluster of four positions on the plot may also be associated with DNA binding. This analysis shows that the base recognition positions can be identified even in the absence of a known structure for a zinc finger. These results are applicable to zinc fingers where the structure of the complex is unknown, in particular suggesting that the individual finger--DNA interaction seen in the Zif268--DNA structure has been conserved in many zinc finger--DNA interactions. |
Databáze: | OpenAIRE |
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