PDBsum entry 1j59

Gene regulation/DNA

PDB id: 1j59

Contents

Protein chains

199 a.a. *

DNA/RNA

Ligands

CMP ×2

Waters ×286

* Residue conservation analysis

PDB id:

1j59

Name:

Gene regulation/DNA

Title:

Catabolite gene activator protein (cap)/DNA complex + adenosine-3',5'- cyclic-monophosphate

Structure:

5'-d( Gp Cp Gp Ap Ap Ap Ap Gp Tp Gp Tp Gp Ap C)-3'. Chain: c, e. Engineered: yes. 5'-d( Ap Tp Ap Tp Gp Tp Cp Ap Cp Ap Cp Tp Tp Tp Tp Cp G )- 3'. Chain: d, f. Engineered: yes. Catabolite gene activator protein (cap). Chain: a, b.

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

2.50Å R-factor: 0.199 R-free: 0.279

Authors:

G.Parkinson,C.Wilson,A.Gunasekera,Y.W.Ebright,R.H.Ebright,H.M.Berman

Key ref:

G.Parkinson et al. (1996). Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface. J Mol Biol, 260, 395-408. PubMed id: 8757802 DOI: 10.1006/jmbi.1996.0409

Date:

01-Mar-02 Release date: 01-Mar-02

Supersedes:

1ber

Protein chains

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

Seq: 210 a.a.

Struc: 199 a.a.

DNA/RNA chains

G-C-G-A-A-A-A-G-T-G-T-G-A-C 14 bases

A-T-A-T-G-T-C-A-C-A-C-T-T-T-T-C-G 17 bases

G-C-G-A-A-A-A-G-T-G-T-G-A-C 14 bases

A-T-A-T-G-T-C-A-C-A-C-T-T-T-T-C-G 17 bases

DOI no: 10.1006/jmbi.1996.0409

J Mol Biol 260:395-408 (1996)

PubMed id: 8757802

Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface.

G.Parkinson, C.Wilson, A.Gunasekera, Y.W.Ebright, R.H.Ebright, R.E.Ebright, H.M.Berman.

ABSTRACT

The crystallographic structure of the CAP-DNA complex at 3.0 A resolution has been reported previously. For technical reasons, the reported structure had been determined using a gapped DNA molecule lacking two phosphates important for CAP-DNA interaction. In this work, we report the crystallographic structure of the CAP-DNA complex at 2.5 A resolution using a DNA molecule having all phosphates important for CAP-DNA interaction. The present resolution permits unambiguous identification of amino acid-base and amino acid-phosphate hydrogen bonded contacts in the CAP-DNA complex. In addition, the present resolution permits accurate definition of the kinked DNA conformation in the CAP-DNA complex.

Selected figure(s)

Figure 1.
Figure 1. (a) DNA site for CAP. There are two conventions for numbering of positions within the DNA site for CAP: convention 1 (Ebright et al., 1984a,b, 1987, 1989; Zhang & Ebright, 1990; Zhang et al., 1991; Gunasekera et al., 1992) and convention 2 (Schultz et al., 1991). In this paper we use convention 1. (b) DNA molecule ``31-2'' used in the previously reported structure of the CAP-DNA complex (Schultz et al., 1990, 1991). DNA molecule ``31-2'' contains symmetry-related single-phosphate gaps between positions 9' and 10' and 13 and 14 (filled bars; see the text). (c) DNA molecule ``31-2E'' used in the present structure of CAP-DNA complex. DNA molecule ``31-2E'' contains symmetry-related single-phosphate gaps between positions 9 and 10 and 13' and 14' (filled bars; see the text).

Figure 4.
Figure 4. Summary of CAP-DNA contacts in the structure of Schultz et al. (1991) (see footnote to p. 000). Contacts in the half-complex A are from Schultz et al. (1991); contacts in the half-complex B are from the inspection of coordinates (Brookhaven Protein Data Bank accession code 1cgp). (b) Summary of the CAP-DNA contacts in the present structure. Contacts to the DNA phosphates missing in the structure of Schultz et al (1991) are in boldface.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 260, 395-408) copyright 1996.