PDBsum entry: 2qj2

Hormone

PDB id: 2qj2

Contents

Protein chains

174 a.a. *

Ligands

SO4 ×4

Waters ×330

* Residue conservation analysis

PDB id:

2qj2

Name:

Hormone

Title:

A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist

Structure:

Hepatocyte growth factor. Chain: a, b. Fragment: residues 28-209. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hgf, hpta. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.81Å R-factor: 0.201 R-free: 0.248

Authors:

W.D.Tolbert,J.Daugherty,C.-F.Gao,Q.Xe,C.Miranti,E.Gherardi, G.Vande Woude,H.E.Xu

Key ref:

W.D.Tolbert et al. (2007). A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist. Proc Natl Acad Sci U S A, 104, 14592-14597. PubMed id: 17804794 DOI: 10.1073/pnas.0704290104

Date:

06-Jul-07 Release date: 18-Sep-07

Protein chains

P14210  (HGF_HUMAN) -  Hepatocyte growth factor

Seq: 728 a.a.

Struc: 174 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: blood coagulation (2 terms)
• Biochemical function: calcium ion binding (2 terms)

DOI no: 10.1073/pnas.0704290104

Proc Natl Acad Sci U S A 104:14592-14597 (2007)

PubMed id: 17804794

A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist.

W.D.Tolbert, J.Daugherty, C.Gao, Q.Xie, C.Miranti, E.Gherardi, G.Vande Woude, H.E.Xu.

ABSTRACT

Hepatocyte growth factor (HGF) activates the Met receptor tyrosine kinase by binding and promoting receptor dimerization. Here we describe a mechanistic basis for designing Met antagonists based on NK1, a natural variant of HGF containing the N-terminal and the first kringle domain. Through detailed biochemical and structural analyses, we demonstrate that both mouse and human NK1 induce Met dimerization via a conserved NK1 dimer interface. Mutations designed to alter the NK1 dimer interface abolish its ability to promote Met dimerization but retain full Met-binding activity. Importantly, these NK1 mutants act as Met antagonists by inhibiting HGF-mediated cell scattering, proliferation, branching, and invasion. The ability to separate the Met-binding activity of NK1 from its Met dimerization activity thus provides a rational basis for designing Met antagonists. This strategy of antagonist design may be applicable for other growth factor receptors by selectively abolishing the receptor activation ability but not the receptor binding of the growth factors.

Selected figure(s)

Figure 2.
Fig. 2. Met dimerization induced by NK1 binding. (A) A diagram of AlphaScreen assay for detecting Met dimerization promoted by NK1 binding. (B) Met dimerization induced by 1 µM NK1 in the presence and absence of 10 µM heparin as measured by AlphaScreen assays. (C) Dose curves of various NK1 to induce Met dimerization in the presence of 10 µM heparin.

Figure 3.
Fig. 3. Crystal structures of the mouse and human NK1. (A) An overall view of the head-to-tail dimer of the mouse NK1. The letters (K, D, Y, and N) indicate the position of residues K85, D123, Y124, and N127, respectively. Only yellow monomer is labeled. (B) The NK1 dimer interface and the intermolecular interactions. The interface within 6.0 Å of the other monomer is shown as a purple surface and inner residues are gold, green, and red if they are within 4.0, 5.0, and 6.0 Å, respectively, of the other NK1. The list of interactions includes non-H-bond packing and H-bond interactions within 4.0 Å between the two NK1 monomers. Double-headed arrows indicate reciprocal interactions between two monomers and single-headed arrows indicate interactions from one monomer to the other. Underlining indicates that the residues' protein backbone atoms are involved in dimer interactions. (C) Interactions mediated by Y124 and K85 (yellow monomer) with V140, D202, I203, and P204 (cyan monomer). Hydrogen bonds are indicated by dashed lines. Water-mediated interactions are indicated by W1 and W2. (D) Interactions mediated by K122, D123, and N127 (yellow monomer) with K122, D123, and N127 (cyan monomer). Hydrogen bonds are indicated by dashed lines. (E) Comparison of the mouse and human NK1 (superposition of the C atoms). The two mouse monomers are in yellow and cyan, and the human monomers are in gold and blue. Arrows indicate the heparin binding sites identified in previous studies (23).

Figures were selected by an automated process.