PDBsum entry: 1o3q

Gene regulation/DNA

PDB-id: 1o3q

Asymmetric unit

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PROCHECK

Protein chain

200 a.a. *

DNA/RNA

Ligands

CMP ×2

Waters ×41

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, hexamer
- as defined in PDB file (see also PQS)

PDB id:

1o3q

Name:

Gene regulation/DNA

Title:

Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes

Structure:

5'-d( Ap Ap Ap Ap Ap Tp Gp Tp Gp Ap T)-3'. Chain: b. Engineered: yes. 5'- d( Cp Tp Ap Gp Ap Tp Cp Ap Cp Ap Tp Tp Tp Tp T)-3'. Chain: c. Engineered: yes. Catabolite gene activator protein. Chain: a.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biological unit:

Hexamer (from PDB file)

UniProt:

P0ACJ8 (CRP_ECOLI)

Seq:

210 a.a.

Struc:

200 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

3.00Å

R-factor:

0.252

R-free:

0.318

Authors:

S.Chen,J.Vojtechovsky,G.N.Parkinson,R.H.Ebright,H.M.Berman

Key ref:

S.Chen et al. (2001). Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.. J Mol Biol, 314, 63-74. [PubMed id: 11724532] [DOI: 10.1006/jmbi.2001.5089]

Date:

18-Mar-03

Release date:

08-Apr-03

Supersedes:

1db7

Related entries:

1o3r
1o3s
1o3t

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Clefts

Surface

Key reference

DOI no: 10.1006/jmbi.2001.5089

J Mol Biol 314:63-74 (2001)

PubMed id: 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.

S.Chen, J.Vojtechovsky, G.N.Parkinson, R.H.Ebright, H.M.Berman.

ABSTRACT

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.

Selected figure(s)

Figure 1.
Figure 1. CAP-DNA complexes having and not having the T:A/G:C base-pair step at the primary-kink site. (a) DNA fragments used for crystallization in space group C222[1]. (b) Least-squares superimposition of structures of CAP-DNA (cyan) and CAP-[6C;17G]DNA (yellow; position 6 of each DNA half-site in red) complexes in space group C222[1]. (c) DNA fragments used for crystallization in space group P3[1]21. (d) Least-squares superimposition of structures of CAP-DNA (blue) and CAP-[6C;17G]DNA (green; position 6 of each DNA half-site in red) complexes in space group P3[1]21. In (a) and (c) the positions of the nicks in the DNA are shown as vertical bars. The o indicates the position of the 2-fold symmetry axis in the sequence. In (b) and (d), CAP is shown in a ribbon representation, and bound cAMP. One molecule per CAP subunit in space group C222[1][13, 14 and 15]; two molecules per CAP subunit in space group P3[1]21. The same positions and the same number of molecules of cAMP were seen in another CAP-DNA complex in a trigonal space group[28]. (b) and (d) were generated using MOLSCRIPT [45].

Figure 3.
Figure 3. Details of CAP-DNA interactions in complexes having and not having the T:A/G:C base-pair step at the primary-kink site. Panels illustrate the second a-helix of the helix-turn-helix motif of CAP (recognition helix) and positions 4 to 8 of the DNA half-site. For reference, the primary-kink is located between position 6 and 7 of the DNA half-site. (a) CAP-DNA (top), CAP-[6C;17G]DNA (middle) and superimposed CAP-DNA and CAP-[6C;17G]DNA (bottom; colors as in Figure 1) complexes in space group C222[1] (half-complex A). (b) CAP-DNA (top), CAP-[6C;17G]DNA (middle) and superimposed CAP-DNA and CAP-[6C;17G]DNA (bottom; colors as in Figure 1) complexes in space group C222[1] (half-complex B). (c) CAP-DNA (top), CAP-[6C;17G]DNA (middle) and superimposed CAP-DNA and CAP-[6C;17G]DNA (bottom; colors as in Figure 1) complexes in space group P3[1]21. Stereodiagrams were generated using MOLSCRIPT[45]. The cutoff distance used for defining hydrogen bonds (violet broken lines) was 3.5 Å.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 63-74) copyright 2001.

Figures were selected by the author.