Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.15 kDa 
• Atom Count: 3212 
• Modelled Residue Count: 357 
• Deposited Residue Count: 370 
• Unique protein chains: 2

2GNJ

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

• DOI: 10.2210/pdb2GNJ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Bos taurus, Oryctolagus cuniculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-04-10 Released: 2006-05-23 
• Deposition Author(s): Bonn, S., Herrero, S., Breitenlechner, C.B., Engh, R.A., Gassel, M., Bossemeyer, D.

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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 

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

• PubMed: 16699172 
• DOI: 10.1074/jbc.M512374200
• Primary Citation of Related Structures:  
  2GFC, 2GNF, 2GNG, 2GNH, 2GNI, 2GNJ, 2GNL


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase, alpha-catalytic subunit	A	350	Bos taurus	Mutation(s): 5  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B [auth I]	20	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for Q3SX13 (Bos taurus) Explore Q3SX13  Go to UniProtKB:  Q3SX13

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y27 (Subject of Investigation/LOI)	C [auth A]	(R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE C14 H21 N3 O IYOZTVGMEWJPKR-IJLUTSLNSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
Y27	BindingDB:  2GNJ	Ki: min: 5000, max: 1.00e+4 (nM) from 2 assay(s)
		IC50: min: 6000, max: 6.00e+4 (nM) from 11 assay(s)
	Binding MOAD:  2GNJ	Ki: 6000 (nM) from 1 assay(s)
	PDBBind:  2GNJ	IC50: 6000 (nM) from 1 assay(s)

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 = 72.69	α = 90
b = 75.48	β = 90
c = 79.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2006-04-10 
• Released Date: 2006-05-23 
Deposition Author(s): Bonn, S., Herrero, S., Breitenlechner, C.B., Engh, R.A., Gassel, M., Bossemeyer, D.

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
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations