2GNJ

PKA three fold mutant model of Rho-kinase with Y-27632


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of protein kinase A mutants with Rho-kinase inhibitor specificity

Bonn, S.Herrero, S.Breitenlechner, C.B.Erlbruch, A.Lehmann, W.Engh, R.A.Gassel, M.Bossemeyer, D.

(2006) J Biol Chem 281: 24818-24830

  • DOI: 10.1074/jbc.M512374200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Controlling aberrant kinase-mediated cellular signaling is a major strategy in cancer therapy; successful protein kinase inhibitors such as Tarceva and Gleevec verify this approach. Specificity of inhibitors for the targeted kinase(s), however, is a ...

    Controlling aberrant kinase-mediated cellular signaling is a major strategy in cancer therapy; successful protein kinase inhibitors such as Tarceva and Gleevec verify this approach. Specificity of inhibitors for the targeted kinase(s), however, is a crucial factor for therapeutic success. Based on homology modeling, we previously identified four amino acids in the active site of Rho-kinase that likely determine inhibitor specificities observed for Rho-kinase relative to protein kinase A (PKA) (in PKA numbering: T183A, L49I, V123M, and E127D), and a fifth (Q181K) that played a surprising role in PKA-PKB hybrid proteins. We have systematically mutated these residues in PKA to their counterparts in Rho-kinase, individually and in combination. Using four Rho-kinase-specific, one PKA-specific, and one pan-kinase-specific inhibitor, we measured the inhibitor-binding properties of the mutated proteins and identify the roles of individual residues as specificity determinants. Two combined mutant proteins, containing the combination of mutations T183A and L49I, closely mimic Rho-kinase. Kinetic results corroborate the hypothesis that side-chain identities form the major determinants of selectivity. An unexpected result of the analysis is the consistent contribution of the individual mutations by simple factors. Crystal structures of the surrogate kinase inhibitor complexes provide a detailed basis for an understanding of these selectivity determinant residues. The ability to obtain kinetic and structural data from these PKA mutants, combined with their Rho-kinase-like selectivity profiles, make them valuable for use as surrogate kinases for structure-based inhibitor design.


    Related Citations: 
    • Protein kinase A in complex with Rho-kinase inhibitors Y-27632, Fasudil, and H-1152P: structural basis of selectivity
      Breitenlechner, C.B., Gassel, M., Hidaka, H., Kinzel, V., Huber, R., Engh, R.A., Bossemeyer, D.
      (2003) Structure 11: 1595

    Organizational Affiliation

    Group of Structural Biochemistry, German Cancer Research Center, 69120 Heidelberg.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunitA350Bos taurusMutation(s): 5 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase inhibitor alphaI20Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q3SX13 (Bos taurus)
Explore Q3SX13 
Go to UniProtKB:  Q3SX13
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y27
Query on Y27

Download CCD File 
A
(R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE
C14 H21 N3 O
IYOZTVGMEWJPKR-IJLUTSLNSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y27Ki:  10000   nM  BindingDB
Y27Ki:  6000   nM  Binding MOAD
Y27IC50:  18000   nM  BindingDB
Y27IC50 :  6000   nM  PDBBind
Y27IC50:  16000   nM  BindingDB
Y27IC50:  60000   nM  BindingDB
Y27IC50:  6000   nM  BindingDB
Y27IC50:  25000   nM  BindingDB
Y27Ki:  5000   nM  BindingDB
Y27IC50:  28000   nM  BindingDB
Y27IC50:  31000   nM  BindingDB
Y27IC50:  9000   nM  BindingDB
Y27IC50:  6000   nM  BindingDB
Y27IC50:  42000   nM  BindingDB
Y27IC50:  12000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.69α = 90
b = 75.48β = 90
c = 79.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Source and taxonomy