PDBsum entry 1ltp

Transcription regulation

PDB id: 1ltp

Contents

Protein chain

262 a.a.

Theoretical model

PDB id:

1ltp

Name:

Transcription regulation

Structure:

Lactose repressor (core protein, residues 62-323) (theoretical model)

Source:

(Escherichia coli)

Authors:

J.C.Nichols,N.K.Vyas,F.A.Quiocho,K.S.Matthews

Key ref:

J.C.Nichols et al. (1993). Model of lactose repressor core based on alignment with sugar-binding proteins is concordant with genetic and chemical data. J Biol Chem, 268, 17602-17612. PubMed id: 8349639

Date:

10-May-93 Release date: 31-Oct-93

Protein chain

No UniProt id for this chain

Struc: 262 a.a.

J Biol Chem 268:17602-17612 (1993)

PubMed id: 8349639

Model of lactose repressor core based on alignment with sugar-binding proteins is concordant with genetic and chemical data.

J.C.Nichols, N.K.Vyas, F.A.Quiocho, K.S.Matthews.

ABSTRACT

Using primary sequence similarity to arabinose-binding protein, D-glucose/D-galactose-binding protein, and ribose-binding protein (Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1991) J. Biol. Chem. 266, 5226-5237; Mowbray, S. L., and Cole, L. B. (1992) J. Mol. Biol. 225, 155-175), the core domain (residues 62-323) of the bacterial regulatory protein lac repressor has been aligned to these sugar-binding proteins of known structure. Although the sequence identity is not striking, there is strong overall homology based on two separate matrix scoring systems (minimum base change per codon (MBC/C) and amino acid homology per residue (AAH/R)) (mean score: MBC/C < 1.25, AAH/R > 5.50; random sequences: MBC/C = 1.45, AAH/R = 4.46). Similarly, the predicted secondary structure of the repressor exhibits excellent agreement with the known secondary structures of the sugar-binding proteins. Using this primary sequence alignment, the tertiary structure of the core domain of the lac repressor has been modeled based on the known structures of the sugar-binding proteins as templates. While the structure deduced for the repressor is hypothetical, the model generated allows a comparison between the predicted tertiary arrangement and the wealth of genetic and chemical data elucidated for the repressor. Important residues involved in operator and sugar binding and in protein assembly have been identified using genetic methods, and placement of these residues in the model is consistent with their known function. This approach, therefore, provides a means to visualize the core domain of the lac repressor that allows interpretation of genetic and chemical data for specific residues and rational design of future experiments.