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

References listed in PDB file

Key reference

Title

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

Authors

C.E.Bell, M.Lewis.

Ref.

Nat Struct Biol, 2000, 7, 209-214. [DOI no: 10.1038/73317]

PubMed id

10700279

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.

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.

Secondary reference #1

Title

Crystal structure of the lactose operon repressor and its complexes with DNA and inducer.

Authors

M.Lewis, G.Chang, N.C.Horton, M.A.Kercher, H.C.Pace, M.A.Schumacher, R.G.Brennan, P.Lu.

Ref.

Science, 1996, 271, 1247-1254. [DOI no: 10.1126/science.271.5253.1247]

PubMed id

8638105

Secondary reference #2

Title

Crystal structure of lac repressor core tetramer and its implications for DNA looping.

Authors

A.M.Friedman, T.O.Fischmann, T.A.Steitz.

Ref.

Science, 1995, 268, 1721-1727. [DOI no: 10.1126/science.7792597]

PubMed id

7792597

Secondary reference #3

Title

The solution structure of lac repressor headpiece 62 complexed to a symmetrical lac operator.

Authors

C.A.Spronk, A.M.Bonvin, P.K.Radha, G.Melacini, R.Boelens, R.Kaptein.

Ref.

Structure, 1999, 7, 1483-1492. [DOI no: 10.1016/S0969-2126(00)88339-2]

PubMed id

10647179

Figure 1.
Figure 1. Ensemble of NMR structures of the HP62-DNA complex. (a) Backbone trace of the full HP62-DNA complex. Numbers indicate the residues of HP62. The DNA backbone is shown as a ribbon. (b) Overlay of the 11 final structures of the HP62-DNA complex. Superimposed are all atoms of residues 4-25, 32-58 of both HP62 monomers (red) and the central 18 base pairs of the lac operator (blue). Residues 4-59 of the two monomers and the full lac operator sequence are shown. (c) View perpendicular to (b). This figure was generated using the program Biosym Insightll.

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #4

Title

Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2d and 3d noe data: change of tertiary structure upon binding to the lac operator.

Authors

M.Slijper, A.M.Bonvin, R.Boelens, R.Kaptein.

Ref.

J Mol Biol, 1996, 259, 761-773. [DOI no: 10.1006/jmbi.1996.0356]

PubMed id

8683581

Figure 1.
Figure 1. Residues 3 to 49 of the final set of 32 structures of lac HP56 are shown.

Figure 3.
Figure 3. Characteristic side-chains in the interior (a), and at the surface (b) of the lac HP56 molecule are shown. The side-chains are indicated in yellow, residues 5 to 47 of the backbone are indicated in blue.

The above figures are reproduced from the cited reference with permission from Elsevier