CRYSTAL-STRUCTURE OF AN ENGINEERED CRO MONOMER BOUND NONSPECIFICALLY TO DNA - POSSIBLE IMPLICATIONS FOR NONSPECIFIC-BINDING BY THE WILD-TYPE PROTEIN

Citation
Ra. Albright et al., CRYSTAL-STRUCTURE OF AN ENGINEERED CRO MONOMER BOUND NONSPECIFICALLY TO DNA - POSSIBLE IMPLICATIONS FOR NONSPECIFIC-BINDING BY THE WILD-TYPE PROTEIN, Protein science, 7(7), 1998, pp. 1485-1494
Citations number
45
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biology
Journal title
ISSN journal
0961-8368
Volume
7
Issue
7
Year of publication
1998
Pages
1485 - 1494
Database
ISI
SICI code
0961-8368(1998)7:7<1485:COAECM>2.0.ZU;2-Q
Abstract
The structure has been determined at 3.0 Angstrom resolution of a comp lex of engineered monomeric Cro repressor with a seven-base pair DNA f ragment. 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 mon omer appears to correspond to a sequence-independent mode of associati on. The overall orientation of the protein relative to the DNA is mark edly different from that observed for Cro dimer bound to a consensus o perator. The recognition helix is rotated 48 degrees further out of th e major groove, while the turn region of the helix-turn-helix remains in contact with the DNA backbone. All of the direct base-specific inte ractions seen in the wild-type Cro-operator complex are lost. Virtuall y all of the ionic interactions with the DNA backbone, however, are ma intained, as is the subset of contacts between the DNA backbone and a channel on the protein surface. Overall, 25% less surface area is buri ed at the protein-DNA interface than for half of the wild-type Cro-ope rator complex, and the contacts are more ionic in character due to a r eduction 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 di mer with DNA. In the sequence-specific complex, the DNA is bent, the p rotein dimer undergoes a large hinge-bending motion relative to the un complexed form, and the complex is twofold symmetric. In contrast, in the proposed nonspecific complex the DNA is straight, the protein reta ins a conformation similar to the apo form, and the complex lacks twof old symmetry. The model is consistent with thermodynamic, chemical, an d mutagenic studies, and suggests that hinge bending of the Cro dimer may be critical in permitting the transition from the binding of prote in at generic sites on the DNA to binding at high affinity operator si tes.