Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 183.32 kDa 
• Atom Count: 11571 
• Residue Count: 1370 
• Unique protein chains: 1

2VX3

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

• DOI: 10.2210/pdb2VX3/pdb

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


• Deposited: 2008-06-30 Released: 2008-09-16 
• Deposition Author(s): Roos, A.K., Soundararajan, M., Pike, A.C.W., Federov, O., King, O., Burgess-Brown, N., Philips, C., Filippakopoulos, P., Arrowsmith, C.H., Wikstrom, M., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

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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 

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

• PubMed: 23665168 
• DOI: 10.1016/j.str.2013.03.012
• Primary Citation of Related Structures:  
  2WO6, 3K2L, 2VX3


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A	A, B, C, D	382	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens) Explore Q13627  Go to UniProtKB:  Q13627
NIH Common Fund Data Resources
PHAROS  Q13627 GTEx  ENSG00000157540

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D15	A, B, C, D	N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide C24 H22 Cl N5 O2 JDGOPNUGILVNJZ-IBGZPJMESA-N
P6G	A, B, C, D	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A, B, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A,B,C,D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

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 = 264.203	α = 90
b = 65.105	β = 115.44
c = 140.282	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-30 
• Released Date: 2008-09-16 
Deposition Author(s): Roos, A.K., Soundararajan, M., Pike, A.C.W., Federov, O., King, O., Burgess-Brown, N., Philips, C., Filippakopoulos, P., Arrowsmith, C.H., Wikstrom, M., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

Revision History 

• 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