2r1j

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

spinqualitylabelsall models 2r1j, resolution 1.53Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2r1j is a 4 chain structure with sequence from Enterobacteria phage p22. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Gene: c2 (Enterobacteria phage P22) Resources: FirstGlance, OCA, RCSB, PDBsum Function [RPC2_BPP22] This protein allows the phage to reside inactively in the chromosome of its host bacterium. This lysogenic state is maintained by binding of regulatory protein C2 to the OR and OL operators, preventing transcription of proteins necessary for lytic development. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. P22 c2 repressor-operator complex: mechanisms of direct and indirect readout.,Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams LD Biochemistry. 2008 Feb 26;47(8):2325-38. Epub 2008 Feb 1. PMID:18237194 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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