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PMID: 8078776 Published · ppublish English Journal Article

Stereochemical basis of DNA recognition by Zn fingers.

Nucleic acids research ·Vol. 22 ·No. 16 ·1994-08-25 ·Pages 3397-405

Suzuki M, Gerstein M, Yagi N

Abstract

DNA-recognition rules for Zn fingers are discussed in terms of crystal structures. The rules can explain the DNA-binding characteristics of a number of Zn finger proteins for which there are no crystal structures. The rules have two parts: chemical rules, which list the possible pairings between the 4 DNA bases and the 20 amino acid residues, and stereochemical rules, which describe the specific base positions contacted by several amino acid positions in the Zn finger. It is discussed that to maintain the correct binding geometry, in which the N-terminus of the recognition helix is closer to the DNA than the C-terminus, the residues facing the DNA on the helix must be larger near the C-terminus, and that two different types of fingers (A and B) bind to DNA in distinctly different ways and cover different numbers of base pairs.

MeSH Terms
Amino Acid Sequence Arginine/metabolism Binding Sites Crystallization DNA/chemistry,metabolism DNA-Binding Proteins/chemistry,metabolism Drosophila Proteins Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Secondary Regulatory Sequences, Nucleic Acid Repressor Proteins Structure-Activity Relationship Transcription Factor TFIIIA Transcription Factors/chemistry,metabolism Zinc Fingers
Chemicals
DNA-Binding Proteins Drosophila Proteins Repressor Proteins Transcription Factor TFIIIA Transcription Factors ttk protein, Drosophila DNA Arginine
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Suzuki M
MRC Laboratory of Molecular Biology, Cambridge, UK.
Gerstein M
Yagi N
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/22.16.3397
Published
1994-08-25
Pages
3397-405
Language
English
Region
England
NLM ID
0411011
PMCID
PMC523735
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/22.16.3397 PMC Full Text View journal details
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