3C2P

X-ray crystal structure of the N4 mini-vRNAP P1 promoter complex

Summary for 3C2P

• Entry DOI: 10.2210/pdb3c2p/pdb
• Related: 3C3L 3C42 3C46 3C47
• Descriptor: P1 Promoter DNA, Virion RNA polymerase (3 entities in total)
• Functional Keywords: protein-dna complex, nucleotidyltransferase, promoter binary complex, dna-hairpin, virion rna polymerase, transferase-dna complex, transferase/dna
• Biological source: Bacteriophage N4
• Cellular location: Virion : Q859P9
• Total number of polymer chains: 4
• Total formula weight: 266339.72

Authors

Gleghorn, M.L.,Murakami, K.S. (deposition date: 2008-01-25, release date: 2008-12-09, Last modification date: 2024-02-21)

Primary citation

Gleghorn, M.L.,Davydova, E.K.,Rothman-Denes, L.B.,Murakami, K.S.
Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.
Mol.Cell, 32:707-717, 2008

PubMed Abstract: Coliphage N4 virion-encapsidated RNA polymerase (vRNAP) is a member of the phage T7-like single-subunit RNA polymerase (RNAP) family. Its central domain (mini-vRNAP) contains all RNAP functions of the full-length vRNAP, which recognizes a 5 to 7 base pair stem and 3 nucleotide loop hairpin DNA promoter. Here, we report the X-ray crystal structures of mini-vRNAP bound to promoters. Mini-vRNAP uses four structural motifs to recognize DNA sequences at the hairpin loop and stem and to unwind DNA. Despite their low sequence similarity, three out of four motifs are shared with T7 RNAP that recognizes a double-stranded DNA promoter. The binary complex structure and results of engineered disulfide linkage experiments reveal that the plug and motif B loop, which block the access of template DNA to the active site in the apo-form mini-vRNAP, undergo a large-scale conformational change upon promoter binding, explaining the restricted promoter specificity that is critical for N4 phage early transcription.

PubMed: 19061645
DOI: 10.1016/j.molcel.2008.11.010

Experimental method

X-RAY DIFFRACTION (2 Å)