PDBsum entry 1gmn

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hormone/growth factor PDB id
Protein chains
170 a.a. *
113 a.a. *
EPE ×2
Waters ×67
* Residue conservation analysis
PDB id:
Name: Hormone/growth factor
Title: Crystal structures of nk1-heparin complexes reveal the basis for nk1 activity and enable engineering of potent agonists of the met receptor
Structure: Hepatocyte growth factor. Chain: a, b. Fragment: nk1. Synonym: scatter factor, sf, hepatopoeitin a. Engineered: yes. Mutation: yes. Other_details: nk1 dimer in complex with heparin molecule
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Biol. unit: Dimer (from PDB file)
2.30Å     R-factor:   0.262     R-free:   0.279
Authors: D.Lietha,D.Y.Chirgadze,B.Mulloy,T.L.Blundell,E.Gherardi
Key ref:
D.Lietha et al. (2001). Crystal structures of NK1-heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the MET receptor. EMBO J, 20, 5543-5555. PubMed id: 11597998 DOI: 10.1093/emboj/20.20.5543
19-Sep-01     Release date:   02-Oct-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P14210  (HGF_HUMAN) -  Hepatocyte growth factor
728 a.a.
170 a.a.*
Protein chain
Pfam   ArchSchema ?
P14210  (HGF_HUMAN) -  Hepatocyte growth factor
728 a.a.
113 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 14 residue positions (black crosses)


DOI no: 10.1093/emboj/20.20.5543 EMBO J 20:5543-5555 (2001)
PubMed id: 11597998  
Crystal structures of NK1-heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the MET receptor.
D.Lietha, D.Y.Chirgadze, B.Mulloy, T.L.Blundell, E.Gherardi.
NK1 is a splice variant of the polypeptide growth factor HGF/SF, which consists of the N-terminal (N) and first kringle (K) domain and requires heparan sulfate or soluble heparin for activity. We describe two X-ray crystal structures of NK1-heparin complexes that define a heparin-binding site in the N domain, in which a major role is played by R73, with further contributions from main chain atoms of T61, K63 and G79 and the side chains of K60, T61, R76, K62 and K58. Mutagenesis experiments demonstrate that heparin binding to this site is essential for dimerization in solution and biological activity of NK1. Heparin also comes into contact with a patch of positively charged residues (K132, R134, K170 and R181) in the K domain. Mutation of these residues yields NK1 variants with increased biological activity. Thus, we uncover a complex role for heparan sulfate in which binding to the primary site in the N domain is essential for biological activity whereas binding to the K domain reduces activity. We exploit the interaction between heparin and the K domain site in order to engineer NK1 as a potent receptor agonist and suggest that dual (positive and negative) control may be a general mechanism of heparan sulfate-dependent regulation of growth factor activity.
  Selected figure(s)  
Figure 3.
Figure 3 Interaction of NK1 with heparin. (A) Stereoview of interactions between heparin monosaccharide units GlcN-5, IdoA-6, GlcN-7 and IdoA-8 with the N domain of NK1. The side chains of R73, K60 and T61 are shown along with conserved hydrogen bonds (in green). (B) Hydrogen bonding network and hydrophobic contacts between the N domain and heparin in crystal type A (left) and type B (right). Most hydrogen bonds occur in both crystal forms; crystal type A shows additional bonds from the side chains of Lys58 and Lys62. (C) The interface between the K domain of protomer F and heparin chain X. Side chains contributing to ionic interactions are shown. The interaction between K170 and heparin is not apparent in this structure, but is seen in several others.
Figure 4.
Figure 4 Heparin-induced oligomerization of wt- and mutant-NK1. (A) The mutations introduced in the N (HP11, HP12) and K domain (1K1, 1K2) of NK1. (B) Cross-linking of wt- and mutant-NK1 in the absence or presence of equimolar concentrations of 14mer heparin. Cross-linked proteins were analysed by western blotting and detected with an anti-HGF/SF polyclonal antibody (1W53). The position of molecular weight markers is also shown. (C -F) Gel filtration of wt- and mutant-NK1 in the absence or presence of equimolar concentrations of 14mer heparin. Chromatography was carried out on an HR30 Superdex-200 column equilibrated in PBS adjusted to 300 mM NaCl. The elution profile of the 1K1 mutant was identical to that of 1K2 and is not shown. wt-NK1 without heparin shows slight retardation in elution volume due to residual interaction with the column. Heparin induced a shift in the elution volume of wt-NK1 and of the K domain mutants but not of the N domain mutants HP11 and HP12.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 5543-5555) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20462834 I.Cañadas, F.Rojo, M.Arumí-Uría, A.Rovira, J.Albanell, and E.Arriola (2010).
C-MET as a new therapeutic target for the development of novel anticancer drugs.
  Clin Transl Oncol, 12, 253-260.  
20639469 R.Sinha Roy, S.Soni, R.Harfouche, P.R.Vasudevan, O.Holmes, Jonge, A.Rowe, A.Paraskar, D.M.Hentschel, D.Chirgadze, T.L.Blundell, E.Gherardi, R.A.Mashelkar, and S.Sengupta (2010).
Coupling growth-factor engineering with nanotechnology for therapeutic angiogenesis.
  Proc Natl Acad Sci U S A, 107, 13608-13613.  
20624990 W.D.Tolbert, J.Daugherty-Holtrop, E.Gherardi, G.Vande Woude, and H.E.Xu (2010).
Structural basis for agonism and antagonism of hepatocyte growth factor.
  Proc Natl Acad Sci U S A, 107, 13264-13269.
PDB codes: 3hmr 3hms 3hmt 3hn4
19114710 J.A.Deakin, B.S.Blaum, J.T.Gallagher, D.Uhrín, and M.Lyon (2009).
The Binding Properties of Minimal Oligosaccharides Reveal a Common Heparan Sulfate/Dermatan Sulfate-binding Site in Hepatocyte Growth Factor/Scatter Factor That Can Accommodate a Wide Variety of Sulfation Patterns.
  J Biol Chem, 284, 6311-6321.  
19144372 J.O'Donnell, K.A.Taylor, and M.S.Chapman (2009).
Adeno-associated virus-2 and its primary cellular receptor--Cryo-EM structure of a heparin complex.
  Virology, 385, 434-443.  
18493641 E.Gemma, O.Meyer, D.Uhrín, and A.N.Hulme (2008).
Enabling methodology for the end functionalization of glycosaminoglycan oligosaccharides.
  Mol Biosyst, 4, 481-495.  
18065694 E.Sulpice, J.Plouët, M.Bergé, D.Allanic, G.Tobelem, and T.Merkulova-Rainon (2008).
Neuropilin-1 and neuropilin-2 act as coreceptors, potentiating proangiogenic activity.
  Blood, 111, 2036-2045.  
18156180 K.R.Catlow, J.A.Deakin, Z.Wei, M.Delehedde, D.G.Fernig, E.Gherardi, J.T.Gallagher, M.S.Pavão, and M.Lyon (2008).
Interactions of hepatocyte growth factor/scatter factor with various glycosaminoglycans reveal an important interplay between the presence of iduronate and sulfate density.
  J Biol Chem, 283, 5235-5248.  
18359766 N.Fukuhara, J.A.Howitt, S.A.Hussain, and E.Hohenester (2008).
Structural and functional analysis of slit and heparin binding to immunoglobulin-like domains 1 and 2 of Drosophila Robo.
  J Biol Chem, 283, 16226-16234.
PDB codes: 2vr9 2vra
18956887 O.A.Ozhogina, A.Grishaev, E.L.Bominaar, L.Patthy, M.Trexler, and M.Llinás (2008).
NMR solution structure of the neurotrypsin Kringle domain.
  Biochemistry, 47, 12290-12298.
PDB codes: 2k4r 2k51
18511928 P.M.Comoglio, S.Giordano, and L.Trusolino (2008).
Drug development of MET inhibitors: targeting oncogene addiction and expedience.
  Nat Rev Drug Discov, 7, 504-516.  
17594020 E.Gemma, A.N.Hulme, A.Jahnke, L.Jin, M.Lyon, R.M.Müller, and D.Uhrín (2007).
DMT-MM mediated functionalisation of the non-reducing end of glycosaminoglycans.
  Chem Commun (Camb), (), 2686-2688.  
17804794 W.D.Tolbert, J.Daugherty, C.Gao, Q.Xie, C.Miranti, E.Gherardi, G.V.Woude, and H.E.Xu (2007).
A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist.
  Proc Natl Acad Sci U S A, 104, 14592-14597.
PDB codes: 2qj2 2qj4
16699514 E.Papagrigoriou, P.A.McEwan, P.N.Walsh, and J.Emsley (2006).
Crystal structure of the factor XI zymogen reveals a pathway for transactivation.
  Nat Struct Mol Biol, 13, 557-558.
PDB code: 2f83
16834555 R.Sasisekharan, R.Raman, and V.Prabhakar (2006).
Glycomics approach to structure-function relationships of glycosaminoglycans.
  Annu Rev Biomed Eng, 8, 181-231.  
15731407 J.C.Pizarro, B.Vulliez-Le Normand, M.L.Chesne-Seck, C.R.Collins, C.Withers-Martinez, F.Hackett, M.J.Blackman, B.W.Faber, E.J.Remarque, C.H.Kocken, A.W.Thomas, and G.A.Bentley (2005).
Crystal structure of the malaria vaccine candidate apical membrane antigen 1.
  Science, 308, 408-411.
PDB codes: 1w81 1w8k
16129835 T.Bai, M.Becker, A.Gupta, P.Strike, V.J.Murphy, R.F.Anders, and A.H.Batchelor (2005).
Structure of AMA1 from Plasmodium falciparum reveals a clustering of polymorphisms that surround a conserved hydrophobic pocket.
  Proc Natl Acad Sci U S A, 102, 12736-12741.
PDB code: 1z40
15167892 J.Stamos, R.A.Lazarus, X.Yao, D.Kirchhofer, and C.Wiesmann (2004).
Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor.
  EMBO J, 23, 2325-2335.
PDB code: 1shy
15049825 M.Banerjee, J.Copp, D.Vuga, M.Marino, T.Chapman, P.van der Geer, and P.Ghosh (2004).
GW domains of the Listeria monocytogenes invasion protein InlB are required for potentiation of Met activation.
  Mol Microbiol, 52, 257-271.  
15292253 M.Lyon, J.A.Deakin, D.Lietha, E.Gherardi, and J.T.Gallagher (2004).
The interactions of hepatocyte growth factor/scatter factor and its NK1 and NK2 variants with glycosaminoglycans using a modified gel mobility shift assay. Elucidation of the minimal size of binding and activatory oligosaccharides.
  J Biol Chem, 279, 43560-43567.  
14707131 S.Ashikari-Hada, H.Habuchi, Y.Kariya, N.Itoh, A.H.Reddi, and K.Kimata (2004).
Characterization of growth factor-binding structures in heparin/heparan sulfate using an octasaccharide library.
  J Biol Chem, 279, 12346-12354.  
14685170 C.Birchmeier, W.Birchmeier, E.Gherardi, and G.F.Vande Woude (2003).
Met, metastasis, motility and more.
  Nat Rev Mol Cell Biol, 4, 915-925.  
14528000 E.Gherardi, M.E.Youles, R.N.Miguel, T.L.Blundell, L.Iamele, J.Gough, A.Bandyopadhyay, G.Hartmann, and P.J.Butler (2003).
Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor.
  Proc Natl Acad Sci U S A, 100, 12039-12044.  
12847110 T.Merkulova-Rainon, P.England, S.Ding, C.Demerens, and G.Tobelem (2003).
The N-terminal domain of hepatocyte growth factor inhibits the angiogenic behavior of endothelial cells independently from binding to the c-met receptor.
  J Biol Chem, 278, 37400-37408.  
12391027 K.Tan, M.Duquette, J.H.Liu, Y.Dong, R.Zhang, A.Joachimiak, J.Lawler, and J.H.Wang (2002).
Crystal structure of the TSP-1 type 1 repeats: a novel layered fold and its biological implication.
  J Cell Biol, 159, 373-382.
PDB code: 1lsl
11799124 M.Delehedde, M.Lyon, R.Vidyasagar, T.J.McDonnell, and D.G.Fernig (2002).
Hepatocyte growth factor/scatter factor binds to small heparin-derived oligosaccharides and stimulates the proliferation of human HaCaT keratinocytes.
  J Biol Chem, 277, 12456-12462.  
11832492 P.Pediaditakis, S.P.Monga, W.M.Mars, and G.K.Michalopoulos (2002).
Differential mitogenic effects of single chain hepatocyte growth factor (HGF)/scatter factor and HGF/NK1 following cleavage by factor Xa.
  J Biol Chem, 277, 14109-14115.  
11891340 S.M.Prince, M.Achtman, and J.P.Derrick (2002).
Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
  Proc Natl Acad Sci U S A, 99, 3417-3421.
PDB code: 1k24
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.