2VX3

Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structures of Down Syndrome Kinases, Dyrks, Reveal Mechanisms of Kinase Activation and Substrate Recognition.

Soundararajan, M.Roos, A.K.Savitsky, P.Filippakopoulos, P.Kettenbach, A.N.Olsen, J.V.Gerber, S.A.Eswaran, J.Knapp, S.Elkins, J.M.

(2013) Structure 21: 986

  • DOI: https://doi.org/10.1016/j.str.2013.03.012
  • Primary Citation of Related Structures:  
    2VX3, 2WO6, 3K2L

  • PubMed Abstract: 

    Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinases (DYRKs) play key roles in brain development, regulation of splicing, and apoptosis, and are potential drug targets for neurodegenerative diseases and cancer. We present crystal structures of one representative member of each DYRK subfamily: DYRK1A with an ATP-mimetic inhibitor and consensus peptide, and DYRK2 including NAPA and DH (DYRK homology) box regions. The current activation model suggests that DYRKs are Ser/Thr kinases that only autophosphorylate the second tyrosine of the activation loop YxY motif during protein translation. The structures explain the roles of this tyrosine and of the DH box in DYRK activation and provide a structural model for DYRK substrate recognition. Phosphorylation of a library of naturally occurring peptides identified substrate motifs that lack proline in the P+1 position, suggesting that DYRK1A is not a strictly proline-directed kinase. Our data also show that DYRK1A wild-type and Y321F mutant retain tyrosine autophosphorylation activity.


  • Organizational Affiliation

    Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
A, B, C, D
382Homo sapiensMutation(s): 0 
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
GTEx:  ENSG00000157540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D15
Query on D15

Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
K [auth B],
T [auth C]
N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide
C24 H22 Cl N5 O2
JDGOPNUGILVNJZ-IBGZPJMESA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
CA [auth D]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
CA [auth D],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
V [auth C]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth D]
J [auth A]
P [auth B]
Q [auth B]
R [auth B]
DA [auth D],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth D]
EA [auth D]
F [auth A]
FA [auth D]
L [auth B]
BA [auth D],
EA [auth D],
F [auth A],
FA [auth D],
L [auth B],
S [auth B],
U [auth C],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.203α = 90
b = 65.105β = 115.44
c = 140.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-12-05
    Changes: Database references
  • Version 1.3: 2013-06-26
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description