2P0C

Catalytic Domain of the Proto-oncogene Tyrosine-protein Kinase MER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

Huang, X.Finerty, P.Walker, J.R.Butler-Cole, C.Vedadi, M.Schapira, M.Parker, S.A.Turk, B.E.Thompson, D.A.Dhe-Paganon, S.

(2009) J Struct Biol 165: 88-96

  • DOI: 10.1016/j.jsb.2008.10.003
  • Primary Citation of Related Structures:  
    3BPR, 3BRB, 2P0C

  • PubMed Abstract: 
  • The mammalian ortholog of the retroviral oncogene v-Eyk, and a receptor tyrosine kinase upstream of antiapoptotic and transforming signals, Mer (MerTK) is a mediator of the phagocytic process, being involved in retinal and immune cell clearance and platelet aggregation ...

    The mammalian ortholog of the retroviral oncogene v-Eyk, and a receptor tyrosine kinase upstream of antiapoptotic and transforming signals, Mer (MerTK) is a mediator of the phagocytic process, being involved in retinal and immune cell clearance and platelet aggregation. Mer knockout mice are viable and are protected from epinephrine-induced pulmonary thromboembolism and ferric chloride-induced thrombosis. Mer overexpression, on the other hand, is associated with numerous carcinomas. Although Mer adaptor proteins and signaling pathways have been identified, it remains unclear how Mer initiates phagocytosis. When bound to its nucleotide cofactor, the high-resolution structure of Mer shows an autoinhibited alphaC-Glu-out conformation with insertion of an activation loop residue into the active site. Mer complexed with compound-52 (C52: 2-(2-hydroxyethylamino)-6-(3-chloroanilino)-9-isopropylpurine), a ligand identified from a focused library, retains its DFG-Asp-in and alphaC-Glu-out conformation, but acquires other conformational changes. The alphaC helix and DFGL region is closer to the hinge region and the ethanolamine moiety of C52 binds in the groove formed between Leu593 and Val601 of the P-loop, causing a compression of the active site pocket. These conformational states reveal the mechanisms of autoinhibition, the pathophysiological basis of disease-causing mutations, and a platform for the development of chemical probes.


    Related Citations: 
    • Cloning and mRNA expression analysis of a novel human protooncogene, c-mer.
      Graham, D.K., Dawson, T.L., Mullaney, D.L., Snodgrass, H.R., Earp, H.S.
      (1994) Cell Growth Differ 5: 647
    • Erratum
      Graham, D.K., Dawson, T.L., Mullaney, D.L., Snodgrass, H.R., Earp, H.S.
      (1994) Cell Growth Differ 5: 1022
    • Mutations in MERTK, the human orthologue of the RCS rat retinal dystrophy gene, cause retinitis pigmentosa.
      Gal, A., Li, Y., Thompson, D.A., Weir, J., Orth, U., Jacobson, S.G., Apfelstedt-Sylla, E., Vollrath, D.
      (2000) Nat Genet 26: 270

    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Ont., Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase MERA, B313Homo sapiensMutation(s): 0 
Gene Names: MERTKMER
EC: 2.7.10.1
Find proteins for Q12866 (Homo sapiens)
Explore Q12866 
Go to UniProtKB:  Q12866
NIH Common Fund Data Resources
PHAROS:  Q12866
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
D [auth A], H [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
E [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], F [auth B], G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.47α = 90
b = 90.057β = 102.44
c = 69.253γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance