1akh
From Proteopedia
(New page: 200px<br /><applet load="1akh" size="450" color="white" frame="true" align="right" spinBox="true" caption="1akh, resolution 2.500Å" /> '''MAT A1/ALPHA2/DNA T...) |
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| - | [[Image:1akh.gif|left|200px]]<br /><applet load="1akh" size=" | + | [[Image:1akh.gif|left|200px]]<br /><applet load="1akh" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1akh, resolution 2.500Å" /> | caption="1akh, resolution 2.500Å" /> | ||
'''MAT A1/ALPHA2/DNA TERNARY COMPLEX'''<br /> | '''MAT A1/ALPHA2/DNA TERNARY COMPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the heterodimer formed by the DNA binding domains | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1AKH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http:// | + | 1AKH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKH OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Jin, Y.]] | [[Category: Jin, Y.]] | ||
[[Category: Li, T.]] | [[Category: Li, T.]] | ||
| - | [[Category: Vershon, A | + | [[Category: Vershon, A K.]] |
[[Category: Wolberger, C.]] | [[Category: Wolberger, C.]] | ||
[[Category: complex]] | [[Category: complex]] | ||
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[[Category: transcription regulation]] | [[Category: transcription regulation]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:45:29 2008'' |
Revision as of 09:45, 21 February 2008
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MAT A1/ALPHA2/DNA TERNARY COMPLEX
Overview
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.
About this Structure
1AKH is a Protein complex structure of sequences from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
Reference
Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract., Li T, Jin Y, Vershon AK, Wolberger C, Nucleic Acids Res. 1998 Dec 15;26(24):5707-18. PMID:9838003
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