PDBsum entry 1si5

Hormone/growth factor

PDB id: 1si5

Contents

Protein chain

227 a.a. *

Waters ×33

* Residue conservation analysis

PDB id:

1si5

Name:

Hormone/growth factor

Title:

Protease-like domain from 2-chain hepatocyte growth factor

Structure:

Hepatocyte growth factor. Chain: h. Fragment: protease-like domain. Synonym: scatter factor. Sf. Hepatopoeitin a. Lung fibroblast-derived mitogen. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108

Resolution:

2.53Å R-factor: 0.248 R-free: 0.301

Authors:

D.Kirchhofer,X.Yao,M.Peek,C.Eigenbrot,M.T.Lipari,K.L.Billeci, H.R.Maun,P.Moran,L.Santell,R.A.Lazarus

Key ref:

D.Kirchhofer et al. (2004). Structural and functional basis of the serine protease-like hepatocyte growth factor beta-chain in Met binding and signaling. J Biol Chem, 279, 39915-39924. PubMed id: 15218027 DOI: 10.1074/jbc.M404795200

Date:

27-Feb-04 Release date: 28-Dec-04

Protein chain

P14210  (HGF_HUMAN) -  Hepatocyte growth factor from Homo sapiens

Seq: 728 a.a.

Struc: 227 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M404795200

J Biol Chem 279:39915-39924 (2004)

PubMed id: 15218027

Structural and functional basis of the serine protease-like hepatocyte growth factor beta-chain in Met binding and signaling.

D.Kirchhofer, X.Yao, M.Peek, C.Eigenbrot, M.T.Lipari, K.L.Billeci, H.R.Maun, P.Moran, L.Santell, C.Wiesmann, R.A.Lazarus.

ABSTRACT

Hepatocyte growth factor (HGF), a plasminogen-related growth factor, is the ligand for Met, a receptor tyrosine kinase implicated in development, tissue regeneration, and invasive tumor growth. HGF acquires signaling activity only upon proteolytic cleavage of single-chain HGF into its alpha/beta heterodimer, similar to zymogen activation of structurally related serine proteases. Although both chains are required for activation, only the alpha-chain binds Met with high affinity. Recently, we reported that the protease-like HGF beta-chain binds to Met with low affinity (Stamos, J., Lazarus, R. A., Yao, X., Kirchhofer, D., and Wiesmann, C. (2004) EMBO J. 23, 2325-2335). Here we demonstrate that the zymogen-like form of HGF beta also binds Met, albeit with 14-fold lower affinity than the protease-like form, suggesting optimal interactions result from conformational changes upon cleavage of the single-chain form. Extensive mutagenesis of the HGF beta region corresponding to the active site and activation domain of serine proteases showed that 17 of the 38 purified two-chain HGF mutants resulted in impaired cell migration or Met phosphorylation but no loss in Met binding. However, reduced biological activities were well correlated with reduced Met binding of corresponding mutants of HGF beta itself in assays eliminating dominant alpha-chain binding contributions. Moreover, the crystal structure of HGF beta determined at 2.53 A resolution provides a structural context for the mutagenesis data. The functional Met binding site is centered on the "active site region" including "triad" and neighboring "activation domain" residues Val(692), Pro(693), Gly(694), Arg(695), and Gly(696) [c214-c219]. Together they define a region that bears remarkable resemblance to substrate processing regions of serine proteases. Models of HGF-dependent Met receptor activation are discussed.

Selected figure(s)

Figure 5.
FIG. 5. HGF x-ray structure and Met binding site. A, structure and electron density of HGF "active site region." The "active site catalytic triad residues" Asp578 [c102]-Gln534 [c57]-Tyr673 [c195] are depicted. Pro693 [c215] adopts a different conformation than Trp [c215] found in serine proteases and partially blocks the entrance to the "S1 pocket," which has a Gly667 [c189] at the bottom. B, stereo view of active site regions of HGF (green) and plasmin (gray). The pseudo-substrate inhibitor Glu-Gly-Arg-chloromethyl ketone from the plasmin structure (yellow) fills the S1 pocket and interacts with its Asp [c189] side chain. The main chain amide nitrogen atoms that stabilize the oxyanion hole (blue spheres) are structurally conserved in HGF . C, location of Met binding site on HGF . Worm depiction of HGF showing mutated residues with <20% (red), 20-60% (orange), 60-80% (yellow), and >80% (blue) of wild type HGF pro-migratory activity data in Fig. 2B. The N terminus and three activation domain loops are in black. Residue Lys649 [c173] would be colored yellow but is disordered in the crystal structure and is not depicted. D, solvent-accessible surface of HGF showing residues colored as in C. The dotted line depicts the Met binding region from the crystal structure of the complex of HGF with the Sema/PSI domains of Met (22).

Figure 6.
FIG. 6. HGF intermolecular contacts and comparison to other proteins. A, intermolecular contacts in HGF x-ray structure. The reference molecule (green) has three crystal contacts. The blue molecule arises from a 2-fold axis relating the N-terminal regions Val496-Arg502 [c17-c23] and adjacent residues. The N-terminal Val495 [c16] of the green and blue molecules are depicted as spheres. The HGF -chain/ -chain interface involving the N terminus and adjacent residues from the [c140] and [c180] loops is shown by the arrow. The salmon-colored molecule arises from a 2-fold axis relating "active site regions." The side chains of Tyr673 [c195] are shown. Residue C604S [c128] (sphere) in the yellow molecule contacts the reference molecule in the [c70] loop. B, partial sequences for HGF and homologous proteins at the border between - and -chains. HGF and chymotrypsinogen numbering are above and below sequences, respectively. The boxed Cys in the -chain forms a disulfide bond with a Cys in the -chain. t-PA, tissue plasminogen activator.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 39915-39924) copyright 2004.

Figures were selected by an automated process.