1o3s: Difference between revisions
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New page: left|200px<br /><applet load="1o3s" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o3s, resolution 3.00Å" /> '''PROTEIN-DNA RECOGNIT... |
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[[Image:1o3s.gif|left|200px]]<br /><applet load="1o3s" size=" | [[Image:1o3s.gif|left|200px]]<br /><applet load="1o3s" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1o3s, resolution 3.00Å" /> | caption="1o3s, resolution 3.00Å" /> | ||
'''PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES'''<br /> | '''PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES'''<br /> | ||
==Overview== | ==Overview== | ||
The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA | The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an "indirect-readout" mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181-->Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7). | ||
==About this Structure== | ==About this Structure== | ||
1O3S is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CMP as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | 1O3S is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CMP:'>CMP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1DB9. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O3S OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Berman, H | [[Category: Berman, H M.]] | ||
[[Category: Chen, S.]] | [[Category: Chen, S.]] | ||
[[Category: Ebright, R | [[Category: Ebright, R H.]] | ||
[[Category: CMP]] | [[Category: CMP]] | ||
[[Category: camp receptor protein]] | [[Category: camp receptor protein]] | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:13:07 2008'' | ||
