PDBsum entry 1r0p

Transferase

PDB id: 1r0p

Contents

Protein chain

301 a.a. *

Ligands

KSA

Waters ×201

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid k-252a.

Authors

N.Schiering, S.Knapp, M.Marconi, M.M.Flocco, J.Cui, R.Perego, L.Rusconi, C.Cristiani.

Ref.

Proc Natl Acad Sci U S A, 2003, 100, 12654-12659. [DOI no: 10.1073/pnas.1734128100]

PubMed id

14559966

Abstract

The protooncogene c-met codes for the hepatocyte growth factor receptor tyrosine kinase. Binding of its ligand, hepatocyte growth factor/scatter factor, stimulates receptor autophosphorylation, which leads to pleiotropic downstream signaling events in epithelial cells, including cell growth, motility, and invasion. These events are mediated by interaction of cytoplasmic effectors, generally through Src homology 2 (SH2) domains, with two phosphotyrosine-containing sequence motifs in the unique C-terminal tail of c-Met (supersite). There is a strong link between aberrant c-Met activity and oncogenesis, which makes this kinase an important cancer drug target. The furanosylated indolocarbazole K-252a belongs to a family of microbial alkaloids that also includes staurosporine. It was recently shown to be a potent inhibitor of c-Met. Here we report the crystal structures of an unphosphorylated c-Met kinase domain harboring a human cancer mutation and its complex with K-252a at 1.8-A resolution. The structure follows the well established architecture of protein kinases. It adopts a unique, inhibitory conformation of the activation loop, a catalytically noncompetent orientation of helix alphaC, and reveals the complete C-terminal docking site. The first SH2-binding motif (1349YVHV) adopts an extended conformation, whereas the second motif (1356YVNV), a binding site for Grb2-SH2, folds as a type II Beta-turn. The intermediate portion of the supersite (1353NATY) assumes a type I Beta-turn conformation as in an Shc-phosphotyrosine binding domain peptide complex. K-252a is bound in the adenosine pocket with an analogous binding mode to those observed in previously reported structures of protein kinases in complex with staurosporine.

Figure 1.
Fig. 1. (a)C^ plot of c-Met in complex with K-252a. The inhibitor is green. The model extends from residues 1050 to 1360. Disordered and not included in the model are residues 1100-1103 (apo-Met: 1099-1103) and residues 1286-1291 (1286-1290), as well as the A-loop residues 1231-1244 in apo c-Met. Residues mutated in human cancer are highlighted with their C^ atoms in red. (b) A view of parts of the N lobe and the A loop. Carbonyl carbon positions of residues mentioned in the discussion are shown as green spheres. A is blue, Cis orange, their flanking regions (including part of 3 that precedes C) are yellow, and the N-terminal portion of the A loop is red. (c) A view of the domain interface as in b. The glycine-rich loop is blue, C is orange, residues 1190-1221 (including the C terminus of E and the catalytic loop) are yellow, and the A loop is red. Red labels indicate the residues mutated in our study. (d) Surface of c-Met:K-252a with the A loop shown as a yellow ribbon. Also shown are parts of the bound inhibitor, as well as side chains for Phe-1234 and Asp-1235. For comparison, the A loops in IRK0P (blue; also shown is Y1162, PDB ID code 1IRK [PDB] ; ref. 23) and FGFRK (red; PDB ID code 1FGI [PDB] ; ref. 43) are shown. All figures were prepared by using ICM (44).

Figure 2.
Fig. 2. (a) Chemical structures of K-252a and staurosporine. The carbazole ring system is blue, and the sugar moieties (pyranose in staurosporine and furanose in K-252a, respectively) are red. The lactam and indole rings are black. (b)2F[o]-F[c]electron density map of the K-252a-binding site contoured at 1.5 . Hydrogen bonds are indicated. (c) c-Met inhibitor binding site. Carbon atoms of c-Met:K-252a are gray and apo-Met atoms are magenta. Carbonyl oxygens were omitted for clarity. K-252a carbons are yellow.