1o3s
From Proteopedia
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|PDB= 1o3s |SIZE=350|CAPTION= <scene name='initialview01'>1o3s</scene>, resolution 3.00Å | |PDB= 1o3s |SIZE=350|CAPTION= <scene name='initialview01'>1o3s</scene>, resolution 3.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CMP:ADENOSINE-3 | + | |LIGAND= <scene name='pdbligand=CMP:ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE'>CMP</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:00:09 2008'' |
Revision as of 11:00, 23 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
Overview
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
1O3S is a Single protein structure of sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1DB9. Full crystallographic information is available from OCA.
Reference
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking., Chen S, Gunasekera A, Zhang X, Kunkel TA, Ebright RH, Berman HM, J Mol Biol. 2001 Nov 16;314(1):75-82. PMID:11724533
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