1. Volume 24, Issue 1, Pages 149-156 (October 2006)
Structural Basis for Processivity and Single-Strand Specificity of RNase II 
Yuhong Zuo, Helen A. Vincent, Jianwei Zhang, Yong Wang, Murray P. Deutscher, Arun Malhotra 
Molecular Cell 
Volume 24, Issue 1, Pages (October 2006)
DOI: /j.molcel
Copyright © 2006 Elsevier Inc. Terms and Conditions

2. Figure 1 The Structure of RNase II
(A) Schematic representation of the primary structure of RNase II and paralogue RNase R. The structural domains are colored the same way as in the ribbon diagrams in all the figures: blue (OB1 domain), cyan (OB2 domain), red (OB3 domain), yellow (helical subdomain of the catalytic domain), green (β-barrel subdomain of the catalytic domain), and orange (the rest of the catalytic domain).
(B) Stereoview of the RNase II structure. A purple ball, representing a bound metal ion, marks the putative active center.
(C) The three OB domains form a clamp-like assembly (shown as ribbons) on top of the catalytic domain (surface shown in gray).
(D) Structural comparison of the three OB domains in RNase II (blue, cyan, and red, respectively), a cold-shock domain (yellow, Protein Data Bank ID 1MJC), and an S1 domain (green, Protein Data Bank ID 1GO3). Alignment was done with LSQMAN (Kleywegt, 1996), and images were generated using PYMOL (DeLano, 2002).
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions

3. Figure 2 RNase II Active Center
(A) Sequence logo of a loop region featuring four conserved acidic residues based on 282 nonredundant sequences of RNR family members, generated by the WebLogo tool (
(B) Relative activity of RNase II active site mutants, assayed with poly(A).
(C) RNase II accessible surface representation, colored by electrostatic charge using GRASP (Nicholls et al., 1991), in stereo (top) and a rotated cutaway view (bottom) showing the substrate binding channel and putative path for ssRNA and the exiting mononucleotide (dashed lines). Arrow on top of the stereoview marks the entry point for this path, which corresponds to the schematic shown in black in the left panel of Figure 3A. The bound metal ion at the putative active center is marked by a green star.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions

4. Figure 3 Proposed Mechanism for RNase II ssRNA Specificity
(A) A schematic model of RNA substrate pathway into the RNase II active site (red scissors). (Left panel) ssRNA binds through the OB clamp with alternative pathways shown as dashed lines, (middle panel) probable multiple pathways for a RNA duplex as it approaches RNase II (RNB), (right panel) a probable favored path for RNA duplex binding to RNase II in the absence of the N-terminal OB domains (ΔN-RNB).
(B) Effects of the N-terminal OB domains on RNase II activity on a duplex containing RNA substrate.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions