Alternate Modes of Cognate RNA Recognition by Human PUMILIO Proteins

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Alternate Modes of Cognate RNA Recognition by Human PUMILIO Proteins Gang Lu, Traci M. Tanaka Hall Structure Volume 19, Issue 3, Pages 361-367 (March 2011) DOI: 10.1016/j.str.2010.12.019 Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Crystal Structures of Human PUM1-HD and PUM2-HD in Complex with p38α NREa RNA (A) Ribbon diagram of PUM2-HD in complex with p38α NREa (UGUAAAUA). PUM repeats are colored alternately light blue and orange. The RNA is colored according to atom type (gray, carbon; red, oxygen; blue, nitrogen; orange, phosphorus). The fifth RNA base and the side chain of Arg888 are colored cyan. Protein side chains that contact the RNA bases are shown. (B) Superposition of Cα traces of PUM1-HD:p38α NREa (blue) and PUM2-HD:p38α NREa (orange). The two structures are aligned over PUM repeats R4–R8′. The figures were prepared with PyMOL (DeLano, 2002). See also Figure S1 for a stereo view of a PUM2-HD Cα trace. Structure 2011 19, 361-367DOI: (10.1016/j.str.2010.12.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Recognition of the Eighth RNA Base by PUM2 Interaction of PUM repeat 1 of PUM2 with (A) A8 in p38α NREa and (B) C8 in erk2 NRE. (C) Superposition of (A) and (B). Structures are shown as in Figure 1 with the carbon atoms in p38α NREa colored gray and erk2 NRE colored light cyan. Hydrogen bonds are indicated by dashed lines. Structure 2011 19, 361-367DOI: (10.1016/j.str.2010.12.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 Recognition of Purine Bases at the Fifth Position by PUM1 and PUM2 The Hoogsteen edges of the fifth purine bases are recognized by PUM1 and PUM2, as in (A) PUM1:p38α NREa, (B) PUM2:p38α NREa, and (C) PUM2:p38α NREb. Structure 2011 19, 361-367DOI: (10.1016/j.str.2010.12.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 4 Base-Omission Mode of Recognition of the Fifth RNA Base PUM1 and PUM2 can recognize the C5 RNA base with both (A) the base-omission mode in PUM2:erk2 NRE and (B) the 1:1 binding mode in PUM1: erk2 NRE. See also Figure S2 illustrating the recognition of U5 and C5 by PUM1. Structure 2011 19, 361-367DOI: (10.1016/j.str.2010.12.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 5 Different Modes of RNA Binding May Present Alternative Recognition Surfaces for Downstream Effector Proteins Surface representation of PUM1-HD:erk2 NRE (UGUACAUC) in (A) the base-omission mode and (B) the canonical 1:1 mode. RNA bases and protein residues with different conformations in both modes are colored by atom type (green, carbon; red, oxygen; blue, nitrogen; orange, phosphorus), and the rest of the structure is colored gray. Structure 2011 19, 361-367DOI: (10.1016/j.str.2010.12.019) Copyright © 2011 Elsevier Ltd Terms and Conditions