1SI5

Protease-like domain from 2-chain hepatocyte growth factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

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

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

(2004) J Biol Chem 279: 39915-39924

  • DOI: 10.1074/jbc.M404795200
  • Primary Citation of Related Structures:  
    1SI5

  • PubMed 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 ...

    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" residues Gln(534) [c57], Asp(578) [c102], and Tyr(673) [c195] 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.


    Organizational Affiliation

    Department of Physiology, Genentech, Inc., South San Francisco, California 94080, USA. dak@gene.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hepatocyte growth factorA [auth H]240Homo sapiensMutation(s): 1 
Gene Names: HGFHPTA
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens)
Explore P14210 
Go to UniProtKB:  P14210
PHAROS:  P14210
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.7α = 90
b = 63.7β = 90
c = 135.1γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
TRUNCATEdata reduction
AMoREphasing
X-PLORrefinement
HKL-2000data collection
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection