PDBsum entry 3fwe

Transcription regulator

PDB id: 3fwe

Contents

Protein chains

202 a.a. *

Ligands

PRO ×2

Waters ×238

* Residue conservation analysis

PDB id:

3fwe

Name:

Transcription regulator

Title:

Crystal structure of the apo d138l cap mutant

Structure:

Catabolite gene activator. Chain: a, b. Synonym: camp receptor protein, camp regulatory protein. Engineered: yes. Mutation: yes

Source:

Escherichia coli k-12. Organism_taxid: 83333. Strain: dh5a. Gene: b3357, cap, crp, csm, jw5702. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.230 R-free: 0.277

Authors:

H.Sharma,J.Wang,J.Kong,S.Yu,T.Steitz

Key ref:

H.Sharma et al. (2009). Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding. Proc Natl Acad Sci U S A, 106, 16604-16609. PubMed id: 19805344 DOI: 10.1073/pnas.0908380106

Date:

17-Jan-09 Release date: 08-Sep-09

Protein chains

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

Seq: 210 a.a.

Struc: 202 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0908380106

Proc Natl Acad Sci U S A 106:16604-16609 (2009)

PubMed id: 19805344

Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.

H.Sharma, S.Yu, J.Kong, J.Wang, T.A.Steitz.

ABSTRACT

The binding of cAMP to the Escherichia coli catabolite gene activator protein (CAP) produces a conformational change that enables it to bind specific DNA sequences and regulate transcription, which it cannot do in the absence of the nucleotide. The crystal structures of the unliganded CAP containing a D138L mutation and the unliganded WT CAP were determined at 2.3 and 3.6 A resolution, respectively, and reveal that the two DNA binding domains have dimerized into one rigid body and their two DNA recognition helices become buried. The WT structure shows multiple orientations of this rigid body relative to the nucleotide binding domain supporting earlier biochemical data suggesting that the inactive form exists in an equilibrium among different conformations. Comparison of the structures of the liganded and unliganded CAP suggests that cAMP stabilizes the active DNA binding conformation of CAP through the interactions that the N(6) of the adenosine makes with the C-helices. These interactions are associated with the reorientation and elongation of the C-helices that precludes the formation of the inactive structure.

Selected figure(s)

Figure 2.
Comparison of the inactive (Left) and the active forms of CAP (Right). (A) Schematic representation of CAP shows [beta]-strands as arrows and [alpha]-helices as coils. The cAMP is shown in ball and stick representation. DNA is shown as transparent spheres and its bases are colored slate blue. (B) The cAMP binding domains and DNA have been excluded to emphasize the orientations of the DNA binding domains and the C-helices. Residues capping the C- and D-helices and cAMP are shown as ball and stick. In the inactive form, K130 is located at the C termini of the C-helices, whereas in the active form, D138 is located at the N termini of the D-helices. (C) The C terminus of the C-helix, the N terminus of the D-helix, and the hinge residues of one protomer of the inactive and the active form.

Figure 4.
The cAMP induced conformational changes of CAP. The side view of CAP is shown. Structure of the unliganded CAP (Left) and of the liganded CAP (Right). A superposition of these two structures along their C-helices is shown in the middle of the figure. The unliganded structure is solid, whereas the liganded structure is transparent. To emphasize the conformational changes on cAMP binding, only the C-, D-, and F-helices are shown.

Figures were selected by an automated process.