PDBsum entry 1efa

Transcription/DNA

PDB id: 1efa

Contents

Protein chains

328 a.a. *

286 a.a. *

DNA/RNA

Ligands

NPF ×3

Waters ×62

* Residue conservation analysis

PDB id:

1efa

Name:

Transcription/DNA

Title:

Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf

Structure:

DNA (5'- d( Gp Ap Ap T Tp Gp Tp Gp Ap Gp Cp Gp Cp Tp Cp Ap Cp Ap Ap Tp T)-3'). Chain: d, e. Engineered: yes. Lac repressor. Chain: a, b, c. Fragment: residues 1-333. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Decamer (from PQS)

Resolution:

2.60Å R-factor: 0.247 R-free: 0.264

Authors:

C.E.Bell,M.Lewis

Key ref:

C.E.Bell and M.Lewis (2000). A closer view of the conformation of the Lac repressor bound to operator. Nat Struct Biol, 7, 209-214. PubMed id: 10700279 DOI: 10.1038/73317

Date:

07-Feb-00 Release date: 06-Mar-00

Protein chains

P03023  (LACI_ECOLI) -  Lactose operon repressor from Escherichia coli (strain K12)

Seq: 360 a.a.

Struc: 328 a.a.*

Protein chain

P03023  (LACI_ECOLI) -  Lactose operon repressor from Escherichia coli (strain K12)

Seq: 360 a.a.

Struc: 286 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

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

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

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.?

DOI no: 10.1038/73317

Nat Struct Biol 7:209-214 (2000)

PubMed id: 10700279

A closer view of the conformation of the Lac repressor bound to operator.

C.E.Bell, M.Lewis.

ABSTRACT

Crystal structures of the Lac repressor, with and without isopropyithiogalactoside (IPTG), and the repressor bound to operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the operator. However, because of the low resolution of the operator-bound structure (4.8 A), the model for the allosteric transition was presented in terms of structural elements rather than in terms of side chain interactions. Here we have constructed a dimeric Lac repressor and determined its structure at 2.6 A resolution in complex with a symmetric operator and the anti-inducer orthonitrophenylfucoside (ONPF). The structure enables the induced (IPTG-bound) and repressed (operator-bound) conformations of the repressor to be compared in atomic detail. An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition.

Selected figure(s)

Figure 2.
Figure 2. Comparison of the conformations of the Lac repressor bound to operator and inducer. a, Stereo C superposition showing the difference in NH[ 2]-subdomain orientation in the structure of the Lac repressor bound to operator (red) and to IPTG (blue). The least squares superposition minimized the r.m.s.d. of the C atoms of only the CO[2]-subdomains of the core of the repressor (not the NH[2]-subdomains). Residues 1 -61 of the repressor bound to IPTG (not shown) are, in the absence of operator, not seen in structures and are presumed to be mobile with respect to the core. b, Stereo C superposition of an individual NH[2]-subdomain in the structures of the repressor bound to operator (red) and IPTG (blue). Residues for which the largest structural differences occur (>4.5 Å), notably Arg 101, are shown in ball-and-stick representation. Differences in all of these residues arrise from different interactions at the dimer interface in the IPTG-bound and operator-bound conformations of the repressor.

Figure 3.
Figure 3. Interactions of the Lac repressor with operator and ONPF. a, Stereo view of the ONPF binding pocket. The anti-inducer ONPF, and the side chains of residues of the repressor that make contacts to ONPF, are shown in ball-and-stick representation. Hydrogen bonding interactions are shown as dotted lines. For clarity, several hydrophobic residues that line the binding pocket are not shown. b, Stereo view of the interactions between the hinge helices of the repressor and the minor groove of the operator. The two DNA strands are shown in green and yellow, while the two subunits of the repressor are shown in blue and brown. Side chains of the repressor that contact the operator directly are highlighted in ball-and-stick representation. Notice that the two Leu 56 side chains of the repressor wedge into the minor groove, at the center of the operator.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 209-214) copyright 2000.

Figures were selected by an automated process.