Model for interaction with promoter DNA and nascent RNA

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Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme Model for interaction with promoter DNA and nascent RNA. (A) RNAP is represented as a molecular surface, colored by domain as in Figure 1, showing the highly concave shape of its active‐site cleft. The ‘pinky’ specificity loop is depicted as a light blue ribbon of connected Cα atoms. The nucleic acid duplex present in the RNAP cleft is represented as a ribbon (RNA, brown; DNA, magenta), corresponding to the phosphodiester backbone, with cylinders as bases. Its location derives from super‐position of the three β‐strands from the active site from the Taq DNA polymerase–duplex DNA complex (Eom et al., 1996). Of the 14/15mer duplex present in the DNA polymerase structure, 6–8 bases can be accomodated in the cleft of RNAP. (B) A close‐up view of the active‐site cleft found in RNAP with the modeled nucleic acid duplex showing clashes with the N‐terminal domain. This view of RNAP is identical to (A) except that α‐helices are depicted as tubes, β‐strands as arrows. Helices F, G and the adjoining loop (N‐terminal domain) are colored yellow, the active‐site β‐strands are in red and the specificity loop is colored light blue. For clarity, the remaining portions of the RNAP structure are colored grey. The position of residues significant for rNTP binding (GLY542), catalysis (ASP812), promoter interaction (ASN 748) are indicated. The location of GLU148, a residue whose mutation severely disrupts RNA binding and processivity (He et al., 1997) is highlighted. (C) The DNA polymerase from Thermus aquaticus is represented as molecular surface showing its more open active‐site cleft. The surface is colored as in (A). The vestigial 3′‐5′ exonuclease domain is colored in white. For clarity, the 5′ exo‐nuclease domain has been deleted. The DNA from the complex is modeled and colored as in (B). IF THIS IMAGE HAS BEEN PROVIDED BY OR IS OWNED BY A THIRD PARTY, AS INDICATED IN THE CAPTION LINE, THEN FURTHER PERMISSION MAY BE NEEDED BEFORE ANY FURTHER USE. PLEASE CONTACT WILEY'S PERMISSIONS DEPARTMENT ON PERMISSIONS@WILEY.COM OR USE THE RIGHTSLINK SERVICE BY CLICKING ON THE 'REQUEST PERMISSIONS' LINK ACCOMPANYING THIS ARTICLE. WILEY OR AUTHOR OWNED IMAGES MAY BE USED FOR NON-COMMERCIAL PURPOSES, SUBJECT TO PROPER CITATION OF THE ARTICLE, AUTHOR, AND PUBLISHER. EMBO J, Volume: 17, Issue: 14, Pages: 4101-4113, First published: 15 July 1998, DOI: (10.1093/emboj/17.14.4101)