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PDBsum entry 2ivu

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Transferase PDB id
2ivu
Jmol
Contents
Protein chain
289 a.a. *
Ligands
FMT ×2
ZD6
Waters ×71
* Residue conservation analysis
PDB id:
2ivu
Name: Transferase
Title: Crystal structure of phosphorylated ret tyrosine kinase domain complexed with the inhibitor zd6474
Structure: Proto-oncogene tyrosine-protein kinase receptor ret precursor. Chain: a. Fragment: tyrosine kinase domain, residues 705-1013. Synonym: ret receptor, c-ret. Engineered: yes. Other_details: ptr at 905
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.
Biol. unit: Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.193     R-free:   0.248
Authors: P.P.Knowles,J.Murray-Rust,N.Q.Mcdonald
Key ref:
P.P.Knowles et al. (2006). Structure and chemical inhibition of the RET tyrosine kinase domain. J Biol Chem, 281, 33577-33587. PubMed id: 16928683 DOI: 10.1074/jbc.M605604200
Date:
16-Jun-06     Release date:   10-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07949  (RET_HUMAN) -  Proto-oncogene tyrosine-protein kinase receptor Ret
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1114 a.a.
289 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.10.1  - Receptor protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP
+ [protein]-L-tyrosine
= ADP
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein phosphorylation   1 term 
  Biochemical function     transferase activity, transferring phosphorus-containing groups     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M605604200 J Biol Chem 281:33577-33587 (2006)
PubMed id: 16928683  
 
 
Structure and chemical inhibition of the RET tyrosine kinase domain.
P.P.Knowles, J.Murray-Rust, S.Kjaer, R.P.Scott, S.Hanrahan, M.Santoro, C.F.Ibáñez, N.Q.McDonald.
 
  ABSTRACT  
 
The RET proto-oncogene encodes a receptor tyrosine kinase for the glial cell line-derived neurotrophic factor family of ligands. Loss-of-function mutations in RET are implicated in Hirschsprung disease, whereas activating mutations in RET are found in human cancers, including familial medullar thyroid carcinoma and multiple endocrine neoplasias 2A and 2B. We report here the biochemical characterization of the human RET tyrosine kinase domain and the structure determination of the non-phosphorylated and phosphorylated forms. Both structures adopt the same active kinase conformation competent to bind ATP and substrate and have a pre-organized activation loop conformation that is independent of phosphorylation status. In agreement with the structural data, enzyme kinetic data show that autophosphorylation produces only a modest increase in activity. Longer forms of RET containing the juxtamembrane domain and C-terminal tail exhibited similar kinetic behavior, implying that there is no cis-inhibitory mechanism within the RET intracellular domain. Our results suggest the existence of alternative inhibitory mechanisms, possibly in trans, for the autoregulation of RET kinase activity. We also present the structures of the RET tyrosine kinase domain bound to two inhibitors, the pyrazolopyrimidine PP1 and the clinically relevant 4-anilinoquinazoline ZD6474. These structures explain why certain multiple endocrine neoplasia 2-associated RET mutants found in patients are resistant to inhibition and form the basis for design of more effective inhibitors.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. RET kinase structures. A, RET-KD-P (green) and RET-KD-0P (cyan for molecule A and red for molecule B) structures superimposed using the C-lobe C- atoms. The bound nucleotides are shown as sticks. B, RET-KD-P (green), activated IRK (Protein Data Bank code 1IR3; orange), and Kit (Protein Data Bank code 1PKG; blue) structures superimposed using equivalent C-lobe C- atoms. C and D, orthogonal views of the trans-inhibited RET-KD dimer with molecule A in green and molecule B in light green. Their N-terminal helices are red and cyan, respectively. Side chain sticks are shown for Tyr^900 and Tyr^905 (orange), Met^918 (magenta), and Pro^766 (orange). E, main chain hydrogen bond contacts in the complex structure (Protein Data Bank code 1IR3) between IRK (orange) and substrate peptide (cyan). F, main chain hydrogen bond contacts in RET-KD between the Met^918 pocket of molecule A (green) and Pro^766 of molecule B (light green).
Figure 3.
FIGURE 3. Ligand-binding sites. Electron density maps around ZD6474 (A) and PP1 (B) show REFMAC-calculated electron density maps with 2mF[o] - DF[c] contoured at 1 in green and mF[o] - DF[c] contoured at 3 in blue and (in A) contoured at 8 in red. C and D are Ligplot (79) schematic diagrams of ZD6474 and PP1 contacts with RET. Water molecules (W) are shown in cyan. E-G show molecular surfaces of the ligand-binding pockets in RET-KD-P, with the solvent side of the surface white and the inside of the surface blue-green. Ligands are shown in stick form, with carbon atoms magenta for ZD6474 (E), green for AMP (F), and brown for PP1 (G). The Val^804 side chain is highlighted in yellow. The pocket with access that is controlled by Val^804 is in the center of each diagram; a second apparent pocket (^*) in E and G is the result of the Phe^735 side chain being disordered in these two complexes.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 33577-33587) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21474065 N.Jura, X.Zhang, N.F.Endres, M.A.Seeliger, T.Schindler, and J.Kuriyan (2011).
Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms.
  Mol Cell, 42, 9.  
19186126 A.Dixit, A.Torkamani, N.J.Schork, and G.Verkhivker (2009).
Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability.
  Biophys J, 96, 858-874.  
19834613 A.Dixit, L.Yi, R.Gowthaman, A.Torkamani, N.J.Schork, and G.M.Verkhivker (2009).
Sequence and structure signatures of cancer mutation hotspots in protein kinases.
  PLoS One, 4, e7485.  
19081671 A.Torkamani, G.Verkhivker, and N.J.Schork (2009).
Cancer driver mutations in protein kinase genes.
  Cancer Lett, 281, 117-127.  
18845906 B.Yao, X.Liu, H.Liang, T.T.Dong, Z.M.Huang, X.Chen, and J.P.Weng (2009).
A novel mutation (D631del) of the RET gene was associated with MEN2A in a Chinese pedigree.
  Endocr J, 56, 99.  
19451690 M.L.Sos, K.Michel, T.Zander, J.Weiss, P.Frommolt, M.Peifer, D.Li, R.Ullrich, M.Koker, F.Fischer, T.Shimamura, D.Rauh, C.Mermel, S.Fischer, I.Stückrath, S.Heynck, R.Beroukhim, W.Lin, W.Winckler, K.Shah, T.LaFramboise, W.F.Moriarty, M.Hanna, L.Tolosi, J.Rahnenführer, R.Verhaak, D.Chiang, G.Getz, M.Hellmich, J.Wolf, L.Girard, M.Peyton, B.A.Weir, T.H.Chen, H.Greulich, J.Barretina, G.I.Shapiro, L.A.Garraway, A.F.Gazdar, J.D.Minna, M.Meyerson, K.K.Wong, and R.K.Thomas (2009).
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions.
  J Clin Invest, 119, 1727-1740.  
19469690 R.T.Kloos, C.Eng, D.B.Evans, G.L.Francis, R.F.Gagel, H.Gharib, J.F.Moley, F.Pacini, M.D.Ringel, M.Schlumberger, and S.A.Wells (2009).
Medullary thyroid cancer: management guidelines of the American Thyroid Association.
  Thyroid, 19, 565-612.  
18493651 B.G.Perera, and D.J.Maly (2008).
Design, synthesis and characterization of "clickable" 4-anilinoquinazoline kinase inhibitors.
  Mol Biosyst, 4, 542-550.  
18404149 D.M.Goldstein, N.S.Gray, and P.P.Zarrinkar (2008).
High-throughput kinase profiling as a platform for drug discovery.
  Nat Rev Drug Discov, 7, 391-397.  
19060208 H.Chen, C.F.Xu, J.Ma, A.V.Eliseenkova, W.Li, P.M.Pollock, N.Pitteloud, W.T.Miller, T.A.Neubert, and M.Mohammadi (2008).
A crystallographic snapshot of tyrosine trans-phosphorylation in action.
  Proc Natl Acad Sci U S A, 105, 19660-19665.
PDB code: 3cly
18084343 M.Schlumberger, F.Carlomagno, E.Baudin, J.M.Bidart, and M.Santoro (2008).
New therapeutic approaches to treat medullary thyroid carcinoma.
  Nat Clin Pract Endocrinol Metab, 4, 22-32.  
18365214 S.W.Moore, and M.G.Zaahl (2008).
Multiple endocrine neoplasia syndromes, children, Hirschsprung's disease and RET.
  Pediatr Surg Int, 24, 521-530.  
17916994 A.Z.Lai, T.S.Gujral, and L.M.Mulligan (2007).
RET signaling in endocrine tumors: delving deeper into molecular mechanisms.
  Endocr Pathol, 18, 57-67.  
17218019 M.M.Bespalov, and M.Saarma (2007).
GDNF family receptor complexes are emerging drug targets.
  Trends Pharmacol Sci, 28, 68-74.  
17306972 S.R.Hubbard, and W.T.Miller (2007).
Receptor tyrosine kinases: mechanisms of activation and signaling.
  Curr Opin Cell Biol, 19, 117-123.  
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 code is shown on the right.