PDBsum entry: 1lmb

Transcription/DNA

PDB id: 1lmb

Contents

Protein chains

87 a.a. *

92 a.a. *

DNA/RNA

Waters ×140

* Residue conservation analysis

PDB id:

1lmb

Name:

Transcription/DNA

Title:

Refined 1.8 angstrom crystal structure of the lambda repressor-operator complex

Structure:

DNA (5'- d( Ap Ap Tp Ap Cp Cp Ap Cp Tp Gp Gp Cp Gp Gp Tp Gp A p Tp Ap T)-3'). Chain: 1. Engineered: yes. DNA (5'- d( Tp Ap Tp Ap Tp Cp Ap Cp Cp Gp Cp Cp Ap Gp Tp Gp G p Tp Ap T)-3'). Chain: 2.

Source:

Synthetic: yes. Enterobacteria phage lambda. Organism_taxid: 10710

Biol. unit:

Tetramer (from PQS)

Resolution:

1.80Å R-factor: 0.189

Authors:

L.J.Beamer,C.O.Pabo

Key ref:

L.J.Beamer and C.O.Pabo (1992). Refined 1.8 A crystal structure of the lambda repressor-operator complex. J Mol Biol, 227, 177-196. PubMed id: 1387915 DOI: 10.1016/0022-2836(92)90690-L

Date:

05-Nov-91 Release date: 05-Nov-91

Supersedes:

1lrd

Protein chain

P03034  (RPC1_LAMBD) -  Repressor protein CI

Seq: 237 a.a.

Struc: 87 a.a.

Protein chain

P03034  (RPC1_LAMBD) -  Repressor protein CI

Seq: 237 a.a.

Struc: 92 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: DNA binding (2 terms)

DOI no: 10.1016/0022-2836(92)90690-L

J Mol Biol 227:177-196 (1992)

PubMed id: 1387915

Refined 1.8 A crystal structure of the lambda repressor-operator complex.

L.J.Beamer, C.O.Pabo.

ABSTRACT

The crystal structure of the lambda repressor-operator complex has been refined to an R-factor of 18.9% at 1.8 A resolution. This refinement, using data collected at low temperature, has revealed the structure of the N-terminal arm and shows that the interactions of repressor with the two halves of the pseudo-symmetric operator site are significantly different. The two halves of the complex are most similar near the outer edge of the operator site (in a region where the lambda and 434 repressors make similar contacts), but they become increasingly different toward the center of the operator. There are striking differences near the center of the site where it appears that the arm makes significant contacts to only one half of the DNA site. This suggested a new way of aligning the operator sites in phage lambda. The high resolution structure confirms many of the previously noted features of the complex, but also reveals a number of new protein-DNA contacts. It also gives a better view of the extensive H-bonding networks that couple contacts made by different residues and different regions of the protein, and reveals important new details about the helix-turn-helix (HTH) region, and the positions of many water molecules in the complex.

Selected figure(s)

Figure 9.
Figure 9. Structure of the N-terminal arm and Asn55 rom the consensus half site monomer of repressor. LysY and ys4 contact guanines in the major groove of the operator site; Lys5 contacts a phosphate group. Also indicated is a irect peptide backbone to base interaction at Cyt8. Because of the poor electron density for Serl and hrob, which is consistent with biochemical data indicating that they make no important contacts to the DN, the conformations of these resiues should be considered tentative. Figure adapted from Clarke et al. (1991).

Figure 10.
Figure 10. Network of contacts to phosphate groups P, ad Pa. An identical set f contacts is made to P,, and Pa,.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 227, 177-196) copyright 1992.

Figures were selected by the author.