1o3s

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXESPROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

Structural highlights 1o3s is a 3 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1db9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3Å Ligands: Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function CRP_ECOLI This protein complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons. The protein induces a severe bend in the DNA. Acts as a negative regulator of its own synthesis as well as for adenylate cyclase (cyaA), which generates cAMP. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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). 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Catabolite gene activator protein 3D structures

spinqualitylabelsall models 1o3s, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image