4JDI | pdb_00004jdi

Crystal structure of Serine/threonine-protein kinase PAK 4 in complex with Paktide S peptide substrate

• PDB DOI: https://doi.org/10.2210/pdb4JDI/pdb

• Classification: transferase/peptide
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-25 Released: 2014-01-29 
• Deposition Author(s): Ha, B.H., Boggon, T.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.233 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Chen, C., Ha, B.H., Thevenin, A.F., Lou, H.J., Zhang, R., Yip, K.Y., Peterson, J.R., Gerstein, M., Kim, P.M., Filippakopoulos, P., Knapp, S., Boggon, T.J., Turk, B.E.

(2014) Mol Cell 53: 140-147

• PubMed: 24374310 
• DOI: https://doi.org/10.1016/j.molcel.2013.11.013
• Primary Citation Related Structures: 
  4JDH, 4JDI, 4JDJ, 4JDK


• PubMed Abstract: 
  

  Eukaryotic protein kinases are generally classified as being either tyrosine or serine-threonine specific. Though not evident from inspection of their primary sequences, many serine-threonine kinases display a significant preference for serine or threonine as the phosphoacceptor residue. Here we show that a residue located in the kinase activation segment, which we term the "DFG+1" residue, acts as a major determinant for serine-threonine phosphorylation site specificity. Mutation of this residue was sufficient to switch the phosphorylation site preference for multiple kinases, including the serine-specific kinase PAK4 and the threonine-specific kinase MST4. Kinetic analysis of peptide substrate phosphorylation and crystal structures of PAK4-peptide complexes suggested that phosphoacceptor residue preference is not mediated by stronger binding of the favored substrate. Rather, favored kinase-phosphoacceptor combinations likely promote a conformation optimal for catalysis. Understanding the rules governing kinase phosphoacceptor preference allows kinases to be classified as serine or threonine specific based on their sequence.

---

Organizational Affiliation: 
• Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, UK; Ludwig Institute for Cancer Research, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, UK.
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: [e-mail].

Biological Assembly 1  

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: 40.76 kDa 
• Atom Count: 2,561 
• Modeled Residue Count: 296 
• Deposited Residue Count: 353 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	A	346	Homo sapiens	Mutation(s): 0  Gene Names: KIAA1142, PAK4 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens) Explore O96013  Go to UniProtKB:  O96013
PHAROS:  O96013 GTEx:  ENSG00000130669

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Paktide S	B	7	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.233 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/438

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.912	α = 90
b = 61.912	β = 90
c = 181.56	γ = 90

Software Package:

Software Name	Purpose
Executor	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Ha, B.H., Boggon, T.J.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary