Volume 2, Issue 7, Pages 629-640 (July 1994) The refined three-dimensional structure of 3α,20β-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases  Debashis Ghosh, Zdzislaw Wawrzak, Charles M Weeks, William L Duax, Mary Erman  Structure  Volume 2, Issue 7, Pages 629-640 (July 1994) DOI: 10.1016/S0969-2126(00)00064-2

Figure 1 (a) Stereoview of one subunit of the tetramer of 3α,20β-HSD shown as an α-carbon atom trace. The view is nearly along the edge of the central β-sheet. The NAD molecule is shown in pink. (b) Folding topology of 3α,20β-HSD. Helices are represented by circles and strands by triangles. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 1 (a) Stereoview of one subunit of the tetramer of 3α,20β-HSD shown as an α-carbon atom trace. The view is nearly along the edge of the central β-sheet. The NAD molecule is shown in pink. (b) Folding topology of 3α,20β-HSD. Helices are represented by circles and strands by triangles. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 2 Interstrand hydrogen bond formation within the seven-stranded twisted β-sheet that forms the core of the 3α,20β-HSD monomer. Only the backbone atoms of the polypeptide chain are shown. Hydrogen bonds are indicated by dashed lines. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 3 A stereographic diagram of the tetrameric 3α,20β-HSD. The monomers are drawn as α-carbon traces of the polypeptide chains. The colors, yellow, green, blue and red represent subunits A, B, C and D, respectively. (The same color code has been followed throughout this paper.) The non-crystallographic 222 symmetry elements are shown as P, Q and R axes. Four NADH molecules are also shown in pink. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 4 Stereoview of the interface between subunits A (yellow) and C (blue) of 3α,20β-HSD related by the Q-axis. The α-helices α E and α F of the two subunits related by the Q-axis are shown forming a four-helix bundle. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 5 Stereoview of the P-axis interface showing the interactions between two helices (α Gs), two strands (β Gs) and the amino termini. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 6 Salt bridge formation involving Arg160, Glu236 and Lys164 from a monomer near the center of the tetrameric assembly. (a) Multiple isomorphous replacement (MIR) electron density at 3.0 å contoured at 1.0σ. (b) 2Fo–Fc density at 2.6 å with calculated phases, contoured at 1.0σ. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 6 Salt bridge formation involving Arg160, Glu236 and Lys164 from a monomer near the center of the tetrameric assembly. (a) Multiple isomorphous replacement (MIR) electron density at 3.0 å contoured at 1.0σ. (b) 2Fo–Fc density at 2.6 å with calculated phases, contoured at 1.0σ. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 7 Stereoviews of the refined cofactor molecule in the C-subunit shown in (a) within MIR electron density at 3.0 å contoured at 1.0σ and in (b) within a (3Fo– 2Fc) annealed omit map calculated at 2.6 å resolution and contoured at 1.0σ. (c) A stereoview of the protein environment of the cofactor-binding site. Interactions of the NAD molecule with protein atoms are shown by dashed lines. Similar densities and cofactor conformations are observed in other subunits. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 7 Stereoviews of the refined cofactor molecule in the C-subunit shown in (a) within MIR electron density at 3.0 å contoured at 1.0σ and in (b) within a (3Fo– 2Fc) annealed omit map calculated at 2.6 å resolution and contoured at 1.0σ. (c) A stereoview of the protein environment of the cofactor-binding site. Interactions of the NAD molecule with protein atoms are shown by dashed lines. Similar densities and cofactor conformations are observed in other subunits. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 7 Stereoviews of the refined cofactor molecule in the C-subunit shown in (a) within MIR electron density at 3.0 å contoured at 1.0σ and in (b) within a (3Fo– 2Fc) annealed omit map calculated at 2.6 å resolution and contoured at 1.0σ. (c) A stereoview of the protein environment of the cofactor-binding site. Interactions of the NAD molecule with protein atoms are shown by dashed lines. Similar densities and cofactor conformations are observed in other subunits. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 8 (a) The putative steroid-binding cleft and a model of steroid binding in the transition state. A cortisone molecule is modeled in the catalytic cleft. NAD molecules and residues Thr12, Arg16, Asn87, Ser139, Tyr152 and Lys156 that may have important roles in the catalysis are shown in yellow. The Connolly surface of the substrate-binding cleft is shown in color (green = hydrophobic; red = polar oxygen; blue = polar nitrogen; yellow = sulfur). The Cα chains of the monomers are colored as described for Figure 3. The distance between the Tyr152 hydroxyl oxygen and 20-keto oxygen is about 2.0 å. The 20-keto oxygen is also within hydrogen bonding distance (∼ 2.6 å) of the Ser139 hydroxyl. Carbon-20 of the steroid is 2.0 å from the C4 position of the nicotinamide ring. (b) A possible mechanism by which these residues may mediate stereospecific hydride transfer and proton relay processes during the biochemical 20-keto to 20β-hydroxyl conversion. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 8 (a) The putative steroid-binding cleft and a model of steroid binding in the transition state. A cortisone molecule is modeled in the catalytic cleft. NAD molecules and residues Thr12, Arg16, Asn87, Ser139, Tyr152 and Lys156 that may have important roles in the catalysis are shown in yellow. The Connolly surface of the substrate-binding cleft is shown in color (green = hydrophobic; red = polar oxygen; blue = polar nitrogen; yellow = sulfur). The Cα chains of the monomers are colored as described for Figure 3. The distance between the Tyr152 hydroxyl oxygen and 20-keto oxygen is about 2.0 å. The 20-keto oxygen is also within hydrogen bonding distance (∼ 2.6 å) of the Ser139 hydroxyl. Carbon-20 of the steroid is 2.0 å from the C4 position of the nicotinamide ring. (b) A possible mechanism by which these residues may mediate stereospecific hydride transfer and proton relay processes during the biochemical 20-keto to 20β-hydroxyl conversion. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 9 Sequence comparison of relevant short-chain dehydrogenases. The abbreviations used are as follows: 3α,20β-HSD, hydroxysteroid dehydrogenase from Streptomyces hydrogenans; DHPR, rat liver dihydropteridine reductase; 15-HPD, 15-hydroxyprostaglandin dehydrogenase; GDH, glucose dehydrogenase; NODG, nodulation factor; ADH, alcohol dehydrogenase. The alignment is based on sequence homology and available tertiary structures of 3α,20β-HSD and DHPR. The sequence identity with 3α, 20β-HSD ranges from 12% (DHPR) to 35% (GDH and NODG). The prediction for the secondary structure is used as a guide for alignment where the sequence-based alignment is ambiguous. Conserved/semi-conserved residues are shown in upper case letters. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 10 Average isotropic temperature factors of the main-chain and side-chain atoms of amino acid residues in subunit A plotted against the sequence numbers. Peaks in these plots, especially at turn and loop regions between residues 52–55, 59–63, and 186– 210, and at the two termini, are indicative of higher thermal motion. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 11 Ramachandran plot for the four subunits of 3α,20β-HSD from the program PROCHECK [24]. Glycine residues are shown by triangles. Over 88% of 832 non-glycine and non-proline residues are in the most favored regions (A,B,L). Only four Ser150s are marginally in the disallowed region (see text for discussion). Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)

Figure 12 A Luzzati plot [21] of the final model. Lines are drawn for random errors from 0.20 å to 0.50 å, at intervals of 0.05 å. The estimated random positional error from this plot is 0.27 å. The data included in the plot are between 8.0 å and 2.6 å resolution. Structure 1994 2, 629-640DOI: (10.1016/S0969-2126(00)00064-2)