PDBsum entry 1zrf

Gene regulation/DNA

PDB id: 1zrf

Contents

Protein chains

203 a.a. *

DNA/RNA

Ligands

CMP ×4

DIO ×5

Waters ×266

* Residue conservation analysis

PDB id:

1zrf

Name:

Gene regulation/DNA

Title:

4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6c;17g]icap38 DNA

Structure:

5'-d( Ap Tp Tp Tp Cp Gp Ap Ap Ap Ap Ap Tp Gp Cp Gp Ap T)- 3'. Chain: w, y. Engineered: yes. 5'-d( Cp Tp Ap Gp Ap Tp Cp Gp Cp Ap Tp Tp Tp Tp Tp Cp Gp Ap Ap Ap T)-3'. Chain: x, z. Engineered: yes. Catabolite gene activator.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: crp, cap, csm. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.10Å R-factor: 0.225 R-free: 0.266

Authors:

H.M.Berman,A.A.Napoli

Key ref:

A.A.Napoli et al. (2006). Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J Mol Biol, 357, 173-183. PubMed id: 16427082 DOI: 10.1016/j.jmb.2005.12.051

Date:

19-May-05 Release date: 21-Mar-06

Protein chains

P0ACJ8  (CRP_ECOLI) -  DNA-binding transcriptional dual regulator CRP from Escherichia coli (strain K12)

Seq: 210 a.a.

Struc: 203 a.a.

DNA/RNA chains

T-T-C-G-A-A-A-A-A-T-G-C-G-A-T 15 bases

C-T-A-G-A-T-C-G-C-A-T-T-T-T-T-C-G-A-A-A-T 21 bases

T-T-T-C-G-A-A-A-A-A-T-G-C-G-A-T 16 bases

C-T-A-G-A-T-C-G-C-A-T-T-T-T-T-C-G-A-A-A-T 21 bases

DOI no: 10.1016/j.jmb.2005.12.051

J Mol Biol 357:173-183 (2006)

PubMed id: 16427082

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.

A.A.Napoli, C.L.Lawson, R.H.Ebright, H.M.Berman.

ABSTRACT

The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing 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, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3' ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5' to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of approximately 42 degrees, twist angles of approximately 16 degrees ), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of approximately 20 degrees, twist angles of approximately 17 degrees). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, approximately 46 degrees per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, approximately 28 degrees per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.

Selected figure(s)

Figure 2.
Figure 2. Superimposed structures of complexes of CAP with DNA sites containing all possible base-pairs at position 6 of the primary-kink site obtained in this study. CAP is presented in a ribbon representation. DNA is colored as follows: cyan, CAP-DNA; blue, CAP-[6A;17T]DNA; yellow, CAP-[6G;17C]DNA; red, CAP-[6C;17G]DNA. The Figure was generated using PyMol (http://pymol.sourceforge.net/) and nuccyl (http://www.mssm.edu/students/jovinl02/research/nuccyl.html).

Figure 5.
Figure 5. Analysis of crystal structures of wild-type CAP-DNA complexes herein and in the literature. (a) Plot of DNA dihedral angle versus DNA bend angle in crystal structures of wild-type CAP-DNA complexes (squares, crystal form-A; triangles, crystal form-B; diamonds, crystal form-C; circles, crystal form-C'). (b) Plot of CAP residue number versus frequency of involvement in crystal-lattice contacts in crystal structures of wild-type CAP-DNA complexes. (c) Surface representation of CAP showing residues involved in crystal-lattice contacts in at least 35% of crystal structures of wild-type CAP-DNA complexes (circles, with greater diameters indicating higher frequencies of involvement in crystal-lattice contacts), DNA recognition helices (magenta), and transcription activating regions 1 (AR1, blue), 2 (AR2, dark green), and 3 (AR3, olive green).

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2006, 357, 173-183) copyright 2006.

Figures were selected by an automated process.