PDBsum entry 3orc

Gene regulation/DNA

PDB id: 3orc

Contents

Protein chain

65 a.a. *

DNA/RNA

Waters ×3

* Residue conservation analysis

PDB id:

3orc

Name:

Gene regulation/DNA

Title:

Crystal structure of an engineered cro monomer bound nonspecifically to DNA

Structure:

DNA (5'-d( Tp Ap Tp Cp Gp Ap Tp A)-3'). Chain: r, s. Engineered: yes. Other_details: 50% occupancy in the outermost positions. Protein (cro repressor). Chain: a. Engineered: yes. Mutation: yes. Other_details: wildtype cro does not form stable monomers. The

Source:

Synthetic: yes. Enterobacteria phage lambda. Organism_taxid: 10710. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å R-factor: 0.224

Authors:

R.A.Albright,M.C.Mossing,B.W.Matthews

Key ref:

R.A.Albright et al. (1998). Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein. Protein Sci, 7, 1485-1494. PubMed id: 9684880 DOI: 10.1002/pro.5560070701

Date:

23-Apr-98 Release date: 02-Dec-98

Protein chain

P03040  (RCRO_LAMBD) -  Regulatory protein cro from Escherichia phage lambda

Seq: 66 a.a.

Struc: 65 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

T-A-T-C-G-A-T-A 8 bases

T-A-T-C-G-A-T-A 8 bases

DOI no: 10.1002/pro.5560070701

Protein Sci 7:1485-1494 (1998)

PubMed id: 9684880

Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein.

R.A.Albright, M.C.Mossing, B.W.Matthews.

ABSTRACT

The structure has been determined at 3.0 A resolution of a complex of engineered monomeric Cro repressor with a seven-base pair DNA fragment. Although the sequence of the DNA corresponds to the consensus half-operator that is recognized by each subunit of the wild-type Cro dimer, the complex that is formed in the crystals by the isolated monomer appears to correspond to a sequence-independent mode of association. The overall orientation of the protein relative to the DNA is markedly different from that observed for Cro dimer bound to a consensus operator. The recognition helix is rotated 48 degrees further out of the major groove, while the turn region of the helix-turn-helix remains in contact with the DNA backbone. All of the direct base-specific interactions seen in the wild-type Cro-operator complex are lost. Virtually all of the ionic interactions with the DNA backbone, however, are maintained, as is the subset of contacts between the DNA backbone and a channel on the protein surface. Overall, 25% less surface area is buried at the protein DNA interface than for half of the wild-type Cro-operator complex, and the contacts are more ionic in character due to a reduction of hydrogen bonding and van der Waals interactions. Based on this crystal structure, model building was used to develop a possible model for the sequence-nonspecific interaction of the wild-type Cro dimer with DNA. In the sequence-specific complex, the DNA is bent, the protein dimer undergoes a large hinge-bending motion relative to the uncomplexed form, and the complex is twofold symmetric. In contrast, in the proposed nonspecific complex the DNA is straight, the protein retains a conformation similar to the apo form, and the complex lacks twofold symmetry. The model is consistent with thermodynamic, chemical, and mutagenic studies, and suggests that hinge bending of the Cro dimer may be critical in permitting the transition from the binding of protein at generic sites on the DNA to binding at high affinity operator sites.

Selected figure(s)

Figure 2.
Fig. 2. Stereo figure showing the electron density in the region where the sugar-phosphatebackbone oftheDNA (yellow)passes through thechanelonthe surface of the Cro monomer(white).Thepart of theproteinshownincludesPhe58,whichpenetratesinto thehydrophobic core, andtheC-terminalresidues(toAsn61).whichoccupytheminorgroove of he NA. Coefficients are 2F0 - F, andphases are from the refmedmodel The map is contouredat lm.

Figure 8.
Fig. 8. Comparison of thebinding f Crotooperator DNA withtheten- tativemodel for the bindingtononcognate DNA. A: Themodelfornon- specificbindingvewedperpendiculartothe DNA (c.f. Fig. 7A). The right-handmonomer is alignedonthe DNA asinthecomplexof he engineeredCromonomer.Theremainder ofthe dimerwasbuiltassuming theconformation f wild-typeCr(Andersonet al., 1981;Ohlendorfet al., 1998).Terecognitionhelices of bothmonomers,shown in red,arecose to the DNA, butthe contactsaremade y opposite ends fthe helices, and are not equivalent. B: Binding of wild-typeCrotooperator DNA (from Albright & atthews,

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 1485-1494) copyright 1998.

Figures were selected by an automated process.