Nucleic Acids Research, Vol 26, Issue 24 5707-5718, Copyright © 1998 by Oxford University Press
T Li, Y Jin, AK Vershon and C Wolberger
The crystal structure of the heterodimer formed by the DNA binding domains
of the yeast mating type transcription factors, MATa1 and MATalpha2, bound
to a 21 bp DNA fragment has been determined at 2.5 A resolution. The DNA
fragment in the present study differs at four central base pairs from the
DNA sequence used in the previously studied ternary complex. These base
pair changes give rise to a (dA5).(dT5) tract without changing the overall
base composition of the DNA. The resulting A-tract occurs near the center
of the overall 60 degrees bend in the DNA. Comparison of the two structures
shows that the structural details of the DNA bend are maintained despite
the DNA sequence changes. Analysis of the A5-tract DNA subfragment shows
that it contains a bend toward the minor groove centered at one end of the
A- tract. The observed bend is larger than that observed in the crystal
structures of A-tracts embedded in uncomplexed DNA, which are straight and
have been presumed to be quite rigid. Variation of the central DNA base
sequence reverses the two AT base pairs contacted in the minor groove by
Arg7 of the alpha2 N-terminal arm without significantly altering the DNA
binding affinity of the a1/alpha2 heterodimer. The Arg7 side chain
accommodates the sequence change by forming alternate H bond interactions,
in agreement with the proposal that minor groove base pair recognition is
insensitive to base pair reversal. Furthermore, the minor groove spine of
hydration, which stabilizes the narrowed minor groove caused by DNA
bending, is conserved in both structures. We also find that many of the
water-mediated hydrogen bonds between the a1 and alpha2 homeodomains and
the DNA are highly conserved, indicating an important role for water in
stabilization of the a1/alpha2-DNA complex.
ARTICLES
Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract
Department of Biophysics and Biophysical Chemistry and The Howard Hughes Medical Institute,Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Anbanandam, D. C. Albarado, C. T. Nguyen, G. Halder, X. Gao, and S. Veeraraghavan Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain PNAS, November 14, 2006; 103(46): 17225 - 17230. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Mathias, S. E. Hanlon, R. A. O'Flanagan, A. M. Sengupta, and A. K. Vershon Repression of the yeast HO gene by the MAT{alpha}2 and MATa1 homeodomain proteins Nucleic Acids Res., December 14, 2004; 32(22): 6469 - 6478. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Moravek, S. Neidle, and B. Schneider Protein and drug interactions in the minor groove of DNA Nucleic Acids Res., March 1, 2002; 30(5): 1182 - 1191. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Mathias, H. Zhong, Y. Jin, and A. K. Vershon Altering the DNA-binding Specificity of the Yeast Matalpha 2 Homeodomain Protein J. Biol. Chem., August 24, 2001; 276(35): 32696 - 32703. [Abstract] [Full Text] [PDF]
|
|