Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain

Cleary, M. A., Herr, W. (April 1995) Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain. Mol Cell Biol, 15 (4). pp. 2090-100. ISSN 0270-7306 (Print)

URL: http://www.ncbi.nlm.nih.gov/pubmed/7891704

Abstract

DNA binding by the Oct-1 protein is directed by its POU domain, a bipartite DNA-binding domain made up of a POU-specific (POUS) domain and a POU-homeo (POUH) domain, two helix-turn-helix-containing DNA-binding modules that cooperate in DNA recognition. Although the best-characterized DNA target for Oct-1 binding is the octamer sequence ATGCAAAT, Oct-1 also binds a number of different DNA sequence elements. For example, Oct-1 recognizes a form of the herpes simplex virus VP16-responsive TAATGARAT element, called the (OCTA-)TAATGARAT site, that lacks octamer site similarity. Our studies suggest two mechanisms by which Oct-1 achieves flexible DNA sequence recognition. First, an important arginine found in the Oct-1 POUS domain tolerates substitutions of its base contacts within the octamer site. Second, on the (OCTA-)TAATGARAT site, the POUS domain is located on the side of the POUH domain opposite from where it is located on an octamer site. This flexibility of the Oct-1 POU domain in DNA binding also has an impact on its participation in a multiprotein-DNA complex with VP16. We show that Oct-1 POUS domain residues that contact DNA have different effects on VP16-induced complex formation depending on whether the VP16-responsive element involved has overlapping octamer similarity or not.

Item Type: Paper
Uncontrolled Keywords: Amino Acid Sequence Arginine/genetics/metabolism Base Sequence Binding Sites Consensus Sequence DNA/genetics/ metabolism DNA-Binding Proteins/ metabolism Herpes Simplex Virus Protein Vmw65/ metabolism Host Cell Factor C1 Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Octamer Transcription Factor-1 Promoter Regions (Genetics)/ genetics Protein Binding Research Support, U.S. Gov't, P.H.S. Structure-Activity Relationship Transcription Factors/ metabolism
Subjects: bioinformatics > genomics and proteomics > design > amino acid design
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > DNA binding protein
organism description > virus > herpes simplex virus
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Herr lab
Depositing User: Jessica Koos
Date: April 1995
Date Deposited: 15 Aug 2014 18:59
Last Modified: 15 Aug 2014 18:59
PMCID: PMC230436
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30579

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