Atypical Recognition of Particular DNA Sequences by the Archaeal Chromosomal MC1 Protein

The MC1 protein is a chromosomal protein likely involved in the DNA compaction of some methanogenic archaea. This small and monomeric protein, structurally unrelated to other DNA binding proteins, bends DNA sharply. By studying the protein binding to various kinds of kinked DNA, we have previously s...

Full description

Saved in:
Bibliographic Details
Published in:Biochemistry (Easton) 2005-08, Vol.44 (30), p.10369-10377
Main Authors: De Vuyst, Guillaume, Aci, Samia, Genest, Daniel, Culard, Françoise
Format: Article
Language:English
Subjects:
Archaea
Archaeal Proteins - chemistry
Archaeal Proteins - metabolism
Binding Sites
Chromosomal Proteins, Non-Histone - chemistry
Chromosomal Proteins, Non-Histone - metabolism
Consensus Sequence
DNA, Archaeal - chemistry
DNA, Archaeal - metabolism
Gene Library
Methanosarcina
Nucleic Acid Heteroduplexes - chemistry
Nucleic Acid Heteroduplexes - metabolism
Protein Conformation
Ribonucleoproteins - chemistry
Ribonucleoproteins - metabolism
Sequence Alignment
Thermodynamics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The MC1 protein is a chromosomal protein likely involved in the DNA compaction of some methanogenic archaea. This small and monomeric protein, structurally unrelated to other DNA binding proteins, bends DNA sharply. By studying the protein binding to various kinds of kinked DNA, we have previously shown that MC1 is able to discriminate between different deformations of the DNA helix. Here we investigate its capacity to recognize particular DNA sequences by using a SELEX procedure. We find that MC1 is able to preferentially bind to a 15 base pair motif [AAAAACACAC(A/C)CCCC]. The structural parameters of this sequence are characterized by molecular dynamics simulation experiments, and the binding mode of the protein to the DNA is studied by footprinting experiments. Our results strongly suggest that the protein realizes an indirect readout of the DNA sequence by binding to the DNA minor groove.
ISSN:0006-2960
1520-4995
DOI:10.1021/bi0474416