view article
Figure 2
The astacin–fetuin-B complex. (a) Cross-eyed stereo cartoon displaying fetuin-B [colors as in Fig. 1[link](b)] inserted into the active-site cleft of astacin (tan ribbon). The MP is shown after a horizontal ∼90° rotation downwards from the traditional standard orientation of MPs (Gomis-Rüth, Botelho et al., 2012BB32), so the cleft runs from left (nonprimed subsites) to right (primed subsites). The catalytic zinc is shown as a magenta sphere and its astacin ligands as stick models, as are P155 and D156 from fetuin-B. (b) Detail of the final (2mFobs − DFcalc)-type Fourier map at 3.1 Å resolution contoured at 1σ above the threshold, depicting the zinc-binding site of astacin (carbons in tan, zinc ion as a magenta sphere) and the CPDCP-trunk of fetuin B (carbons in pink). (c) Close-up view of (a) after a horizontal 35° rotation, displaying selected residues participating in the interaction between fetuin-B (Cα ribbon in plum; from left to right, segments S146–D162, M111–E114, N197–Y206 and T241–S245; carbons in pink and residue numbers according to UniProt Q9QXC1 in blue) and astacin (Cα ribbon in tan, carbons in orange, catalytic zinc as a magenta sphere and residue numbers in black italics according to UniProt P07584). The C154–C157 disulfide from the CPDCP-trunk of fetuin-B is shown with green sulfurs. (d) Scheme of the proposed `raised elephant-trunk model'; the view mirrors that in (a) and (b). The CPDCP-trunk ([\bigcirc \kern -.7em \scriptstyle 1]) would be the raised trunk (in red) and hairpin I ([\bigcirc \kern -.7em \scriptstyle 2]) and II ([\bigcirc \kern -.7em \scriptstyle 3]) the two front and back limbs (in turquoise), respectively (see top-left inset). The trunk contacts the catalytic zinc ion (magenta sphere) of astacin (in brown) by residues nestling into cleft subsites S4, S3, S2, S2′ and S3′, as shown by purple arrows. Dashed lines represent distantly connected segments or disordered loops. Hydrogen bonds between main-chain atoms, between side-chain and main-chain atoms, and between side-chain atoms are shown as gray, red and blue dashed lines, respectively. The electrostatic interaction between the catalytic zinc and D156 is in light blue. The disulfide connecting the CPDCP-trunk is shown as a green solid line. (e) Superposition of the experimental structure of mouse fetuin-B (white carbons and black labels) and the comparative model of human fetuin-A (cyan carbons and blue labels with regular residue numbers in italics) depicting the regions of the CPDCP warhead and the tips of hairpins I and II of each structure. The view results from (c) after a 90° rotation in the plane. The catalytic zinc ion of astacin is further shown as a magenta sphere for reference.

IUCrJ
Volume 6| Part 2| March 2019| Pages 317-330
ISSN: 2052-2525
https://doi.org/10.1107/S2052252519001568