Volume 9, Issue 12, Pages 1253-1263 (December 2001) Crystal Structure of Human AUH Protein, a Single-Stranded RNA Binding Homolog of Enoyl-CoA Hydratase  Kazuki Kurimoto, Shuya Fukai, Osamu Nureki, Yutaka Muto, Shigeyuki Yokoyama  Structure  Volume 9, Issue 12, Pages 1253-1263 (December 2001) DOI: 10.1016/S0969-2126(01)00686-4

Figure 1 Ribbon Representation of the AUH Hexamer Structure (a) The side view. The 3-fold axis is parallel to the paper. The six subunits are colored gray, orange, green, cyan, yellow, and magenta, respectively. (b) The top view. The 3-fold axis is perpendicular to the paper. The coloring scheme is the same as in (a). Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 2 Ribbon Representation of the AUH and Enoyl-CoA Hydratase Structures (a) Stereo view of the AUH structure. The α and 310 helices are colored brown, while the β strands are colored green. (b) Stereo view of the enoyl-CoA hydratase structure. The coloring scheme is the same as in (a). Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 3 Sequence Alignment of AUH, Enoyl-CoA Hydratase, and Dienoyl-CoA Isomerase The secondary structure elements of AUH are indicated above the sequences. The α and 310 helices are represented with the red and yellow bars, respectively. The β strands are represented with the green arrows. The numbers of the first residues of the secondary structure elements are shown under the bars and the arrows. The H2B α helices of enoyl-CoA hydratase and dienoyl-CoA isomerase, which have lengths that are different from that of AUH, are indicated above the respective sequences. The R peptide is represented with the inverted letters. The catalytic Glu residues are colored red. The residues involved in the trimer-trimer interactions (cutoff 3.5 Å) are represented with the white letters in the orange boxes. Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 4 The Manner of AUH Trimerization (a) Stereo view of the AUH trimer structure, from the viewpoint of the partner trimer. The subunits are colored cyan, yellow, and magenta, respectively. α helices involved in the subunit interactions to form the trimer (H2B, H4B, and H5 of the cyan-colored subunit and H8′ and H10′ of the magenta-colored subunit) are indicated. α helix H1, which faces the partner trimer together with α helices H2B, H8′, and H9′, is also indicated. (b) Stereo view of the AUH trimer structure, from the viewpoint opposite to that in (a). The coloring scheme is the same as in (a). Helices that constitute the active-site pocket (α helices H2A–H3 and 310 helix H4A of the cyan-colored subunit and H9′ and H10′ of the magenta-colored subunit) are indicated. Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 5 Active-Site Pockets of AUH and Enoyl-CoA Hydratase (a) Stereo view of the active-site pocket of AUH. Helices that constitute the active-site pocket (α helices H2A–H3 and 310 helix H4A of the cyan-colored subunit and H9′ and H10′ of the magenta-colored subunit) are indicated. Glu189 and Glu209, which are the counterparts of the catalytic residues of enoyl-CoA hydratase (Glu144* and Glu164*, respectively), are indicated with the stick representation. β strands B2 and B3, which are located around the active-site pocket, are also shown. (b) Stereo view of the active-site pocket of enoyl-CoA hydratase. The coloring scheme is the same as in (a). The catalytic residues, Glu144* and Glu164*, and the acetoacetyl-CoA molecule (gray) are indicated with the stick representation. (c) Close-up stereo view of the active-site pocket of AUH (green) superimposed on that of enoyl-CoA hydratase (yellow). Glu189 and Glu209 of AUH, Glu144* and Glu164* of enoyl-CoA hydratase, and the acetoacetyl-CoA molecule (gray) in the crystal structure of enoyl-CoA hydratase are shown. (d) Stereo view of the σa-weighted 2 |Fo| − |Fc| electron density map of the AUH active-site pocket. Glu189, Glu209, and the water molecule hydrogen bonded to them are indicated. Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 6 The Trimer-Trimer Interactions of AUH, Enoyl-CoA Hydratase, and Dienoyl-CoA Isomerase (a) Ribbon representation of a trimer of AUH, from the viewpoint of the partner trimer. α helices H1 and H2B are colored magenta and orange, respectively. α helices H8 and H9 are colored blue. (b) Surface representation of the AUH trimer, from the viewpoint of the partner trimer. The distances from the partner trimer are color coded from red (3.5 Å) to white (10 Å). (c) Surface representation of the enoyl-CoA hydratase trimer. (d) Surface representation of the dienoyl-CoA isomerase trimer. The coloring schemes of (c) and (d) are the same as in (b). Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 7 Electrostatic Surface Potentials of AUH and Enoyl-CoA Hydratase (a) Surface (upper) and ribbon (lower) representations of the AUH hexamer. The positive and negative charges are shown in blue and red, respectively, in the surface representation. 310 helix H0B and α helices H1, H2A, H2B, H7, and H10 are indicated with the white letters in the surface representation and are colored green, blue, magenta, orange, yellow, and cyan in the ribbon representation, respectively. (b) Surface and ribbon representations of the enoyl-CoA hydratase hexamer. The coloring scheme is the same as in (a). (c) Sequence alignments of AUH and enoyl-CoA hydratase around α helices H1, H2A, H2B, and H7B. α helices H1 and H7B are represented with the red bars above the respective sequences. α helices H2A and H2B of AUH and enoyl-CoA hydratase are shown above and below the sequence, respectively. The acidic and basic amino acid residues are represented with the white letters in the red and blue boxes, respectively. Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)

Figure 8 Proposed RNA Binding Scaffold of AUH (a) The lysine comb. Lys residues on α helix H1 (Lys105, Lys 109, Lys113, and Lys119) are represented with the yellow (carbon atoms) and blue (nitrogen atoms) sticks. (b) RNA binding activities of the GST-tagged wild-type and mutant K105N/K109E/K113Q AUH proteins, demonstrated by SDS-PAGE analysis after UV-crosslinking with 32P-labeled IL-3 ARE RNA. (c) Model of a 6 nucleotide single-stranded polyuridylate molecule bound between the two lysine combs. (d) Model of a long (39 nucleotide), single-stranded polyuridylate molecule winding along the AUH hexamer. In addition to the lysine comb, the basic amino acid residues that may interact with the RNA (Lys122, Lys160, and Lys319) are represented with the yellow and blue sticks. The coloring schemes of (c) and (d) are the same as in (a). Figures 1, 2, 4, 5a–5c, 6a, 7a, 7b (lower figures), 8a, 8c, and 8d were prepared using the programs Molscript [45] and Raster 3D [46]. Figure 5d was prepared using the program DINO (Philippsen, 2000, DINO: Visualizing Structural Biology. http://www.bioz.unibas.ch/~xray/dino). Figures 6b–6d, 7a, and 7b (upper figures) were prepared using the program GRASP [47]. Structure 2001 9, 1253-1263DOI: (10.1016/S0969-2126(01)00686-4)