2R1J

Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T

Summary for 2R1J

• Entry DOI: 10.2210/pdb2r1j/pdb
• Descriptor: 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3', 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3', Repressor protein C2, ... (4 entities in total)
• Functional Keywords: protein-dna complex, helix-turn-helix, dna-binding, repressor, transcription, transcription regulation, transcription-dna complex, transcription/dna
• Biological source: Enterobacteria phage P22
• Total number of polymer chains: 4
• Total formula weight: 27512.80

Authors

Williams, L.D.,Koudelka, G.B.,Watkins, D.,Hsiao, C.,Woods, K. (deposition date: 2007-08-22, release date: 2008-04-29, Last modification date: 2024-02-21)

Primary citation

Watkins, D.,Hsiao, C.,Woods, K.K.,Koudelka, G.B.,Williams, L.D.
P22 c2 repressor-operator complex: mechanisms of direct and indirect readout
Biochemistry, 47:2325-2338, 2008

PubMed Abstract: The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps to direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. We describe the 1.6 A X-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2. This operator has an A-T base pair at position 9L and a T-A base pair at position 9R and is termed DNA9T. Direct readout: nondirectional van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD-DNA9T complex suggests that sequence-specificity arises substantially from lock-and-key interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5'-TTAA-3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational changes. Protein-DNA hydrogen bonding plays a secondary role in specificity. Indirect readout: it is known that the noncontacted bases in the center of the complex are important determinants of affinity. The protein induces a transition of the noncontacted region from B-DNA to B'-DNA. The B' state is characterized by a narrow minor groove and a zigzag spine of hydration. The free energy of the transition from B- to B'-DNA is known to depend on the sequence. Thus, the observed DNA conformation and hydration allows for the formulation of a predictive model of the indirect readout phenomenon.

PubMed: 18237194
DOI: 10.1021/bi701826f

Experimental method

X-RAY DIFFRACTION (1.53 Å)