1o3t: Difference between revisions
New page: left|200px<br /><applet load="1o3t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o3t, resolution 2.80Å" /> '''PROTEIN-DNA RECOGNIT... |
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[[Image:1o3t.gif|left|200px]]<br /><applet load="1o3t" size=" | [[Image:1o3t.gif|left|200px]]<br /><applet load="1o3t" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1o3t, resolution 2.80Å" /> | caption="1o3t, resolution 2.80Å" /> | ||
'''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) makes no direct contact with the | The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 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' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp 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. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence. | ||
==About this Structure== | ==About this Structure== | ||
1O3T 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 | 1O3T 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 1DBC. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O3T 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: Parkinson, G | [[Category: Parkinson, G N.]] | ||
[[Category: Vojtechovsky, J.]] | [[Category: Vojtechovsky, J.]] | ||
[[Category: CMP]] | [[Category: CMP]] | ||
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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 14:13:05 2008'' | ||
Revision as of 15:13, 21 February 2008
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PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
OverviewOverview
The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 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' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp 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. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.
About this StructureAbout this Structure
1O3T is a Single protein structure of sequence from Escherichia coli with as ligand. This structure supersedes the now removed PDB entry 1DBC. Full crystallographic information is available from OCA.
ReferenceReference
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking., Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM, J Mol Biol. 2001 Nov 16;314(1):63-74. PMID:11724532
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