Catalytic domains, superposition

Fig. 8. (a) Structure of the full-length Rieske protein from bovine heart mitochondrial bci complex. The catalytic domain is connected to the transmembrane helix by a flexible linker, (b) Superposition of the three positional states of the catalytic domain of the Rieske protein observed in different crystal forms. The ci state is shown in white, the intermediate state in gray, and the b state in black. Cytochrome b consists of eight transmembrane helices and contains two heme centers, heme and Sh-Cytochrome c i has a water-soluble catalytic domain containing heme c i and is anchored by a C-terminal transmembrane helix. The heme groups are shown as wireframes, the iron atoms as well as the Rieske cluster in the three states as space-filling representations. 

AsnRS, LysRS, and AspRS, the partners of class lib aaRSs, display strong resemblances in the modular organization of their catalytic domain, but superposition reveals angular shifts of the N-terminal domain, which can reach up to 18.8°. ... 

Figure 8. Superposition of the N-terminal domain of thermolysin (silver) and the catalytic domain of collagenase (orange). Stereo ribbon diagram illustrating the common topology between representative structures of the long spacer (silver) and short spacer (orange) families defining the zinc-endoprotease fold.

Figure 14. Zinc endoproteases a structural superfamily. The central panel shows the superposition of the alpha carbon atoms of the topologically equivalent catalytic domains of proteins from the long consensus family (silver) and the short spacer family (orange). Various consensus sequences are given (see text) with the zinc-chelating residues shown in white. Full blue arrows indicate presence of motif in observed three-dimensional structures corresponding to the zinc endoprotease fold shown in the central panel. Dotted lines indicate putative structure-sequence relationships discussed in the text.

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

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