4CSV | pdb_00004csv

Tyrosine kinase AS - a common ancestor of Src and Abl bound to Gleevec

• PDB DOI: https://doi.org/10.2210/pdb4CSV/pdb

• Classification: TRANSFERASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-10 Released: 2015-03-04 
• Deposition Author(s): Kutter, S., Wilson, C., Cruz, L., Agafonov, R.V., Hoemberger, M.S., Zorba, A., Kern, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Kinase Dynamics. Using Ancient Protein Kinases to Unravel a Modern Cancer Drug'S Mechanism.

Wilson, C., Agafonov, R.V., Hoemberger, M., Kutter, S., Zorba, A., Halpin, J., Buosi, V., Otten, R., Waterman, D., Theobald, D.L., Kern, D.

(2015) Science 347: 882

• PubMed: 25700521 
• DOI: https://doi.org/10.1126/science.aaa1823
• Primary Citation Related Structures: 
  4CSV, 4UEU


• PubMed Abstract: 
  

  Macromolecular function is rooted in energy landscapes, where sequence determines not a single structure but an ensemble of conformations. Hence, evolution modifies a protein's function by altering its energy landscape. Here, we recreate the evolutionary pathway between two modern human oncogenes, Src and Abl, by reconstructing their common ancestors. Our evolutionary reconstruction combined with x-ray structures of the common ancestor and pre-steady-state kinetics reveals a detailed atomistic mechanism for selectivity of the successful cancer drug Gleevec. Gleevec affinity is gained during the evolutionary trajectory toward Abl and lost toward Src, primarily by shifting an induced-fit equilibrium that is also disrupted in the clinical T315I resistance mutation. This work reveals the mechanism of Gleevec specificity while offering insights into how energy landscapes evolve.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA.
Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA.
Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.75 kDa 
• Atom Count: 2,061 
• Modeled Residue Count: 244 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC-ABL TYROSINE KINASE ANCESTOR	A	275	synthetic construct	Mutation(s): 0  EC: 2.7.10.2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	B [auth A]	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C29 H31 N7 O KTUFNOKKBVMGRW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.029	α = 90
b = 56.869	β = 116.62
c = 76.118	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Kutter, S., Wilson, C., Cruz, L., Agafonov, R.V., Hoemberger, M.S., Zorba, A., Kern, D.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary