1o3q: Difference between revisions

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, resolution 3.00Å

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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

1O3Q is a Single protein structure of sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1DB7. 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

Page seeded by OCA on Thu Mar 20 13:05:21 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:1o3q.gif|left|200px]]<br /><applet load="1o3q" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1o3q.gif|left|200px]]
-caption="1o3q, resolution 3.00&Aring;" />
-'''PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES'''<br />
+ {{Structure
+|PDB= 1o3q |SIZE=350|CAPTION= <scene name='initialview01'>1o3q</scene>, resolution 3.00&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=CMP:ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE'>CMP</scene>
+|ACTIVITY=
+|GENE=
+}}
+'''PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-O3Q 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 1DB7. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O3Q OCA].
+O3Q is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry 1DB7. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O3Q OCA].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11724532 11724532]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/11724532 11724532]
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
@@ Line 26: / Line 35: @@
 [[Category: protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:13:06 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:05:21 2008''