3QBV

Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin

Summary for 3QBV

• Entry DOI: 10.2210/pdb3qbv/pdb
• Related: 1KI1
• Descriptor: Cell division control protein 42 homolog, Intersectin-1, GUANOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: computationally designed, orthogonal interaction, gtpase, nucleotide exchange, cell membrane, gtp-binding, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, cell junction, cell projection, endocytosis, phosphoprotein, sh3 domain, synapse, synaptosome, protein binding-signaling protein complex, protein binding/signaling protein
• Biological source: Homo sapiens (human); More
• Cellular location: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential): P60953; Endomembrane system (By similarity): Q15811
• Total number of polymer chains: 4
• Total formula weight: 121928.46

Authors

Kapp, G.T.,Remenyi, A.,Lim, W.A.,Kortemme, T. (deposition date: 2011-01-14, release date: 2012-02-08, Last modification date: 2023-09-13)

Primary citation

Kapp, G.T.,Liu, S.,Stein, A.,Wong, D.T.,Remenyi, A.,Yeh, B.J.,Fraser, J.S.,Taunton, J.,Lim, W.A.,Kortemme, T.
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.
Proc.Natl.Acad.Sci.USA, 109:5277-5282, 2012

PubMed Abstract: Signaling pathways depend on regulatory protein-protein interactions; controlling these interactions in cells has important applications for reengineering biological functions. As many regulatory proteins are modular, considerable progress in engineering signaling circuits has been made by recombining commonly occurring domains. Our ability to predictably engineer cellular functions, however, is constrained by complex crosstalk observed in naturally occurring domains. Here we demonstrate a strategy for improving and simplifying protein network engineering: using computational design to create orthogonal (non-crossreacting) protein-protein interfaces. We validated the design of the interface between a key signaling protein, the GTPase Cdc42, and its activator, Intersectin, biochemically and by solving the crystal structure of the engineered complex. The designed GTPase (orthoCdc42) is activated exclusively by its engineered cognate partner (orthoIntersectin), but maintains the ability to interface with other GTPase signaling circuit components in vitro. In mammalian cells, orthoCdc42 activity can be regulated by orthoIntersectin, but not wild-type Intersectin, showing that the designed interaction can trigger complex processes. Computational design of protein interfaces thus promises to provide specific components that facilitate the predictable engineering of cellular functions.

PubMed: 22403064
DOI: 10.1073/pnas.1114487109

Experimental method

X-RAY DIFFRACTION (2.65 Å)