4OLI | pdb_00004oli

The pseudokinase/kinase protein from JAK-family member TYK2

• PDB DOI: https://doi.org/10.2210/pdb4OLI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-01-23 Released: 2014-05-28 
• Deposition Author(s): Eigenbrot, C., Ultsch, M., Wallweber, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.257 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structure of the pseudokinase-kinase domains from protein kinase TYK2 reveals a mechanism for Janus kinase (JAK) autoinhibition.

Lupardus, P.J., Ultsch, M., Wallweber, H., Bir Kohli, P., Johnson, A.R., Eigenbrot, C.

(2014) Proc Natl Acad Sci U S A 111: 8025-8030

• PubMed: 24843152 
• DOI: https://doi.org/10.1073/pnas.1401180111
• Primary Citation Related Structures: 
  4OLI


• PubMed Abstract: 
  

  Janus kinases (JAKs) are receptor-associated multidomain tyrosine kinases that act downstream of many cytokines and interferons. JAK kinase activity is regulated by the adjacent pseudokinase domain via an unknown mechanism. Here, we report the 2.8-Å structure of the two-domain pseudokinase-kinase module from the JAK family member TYK2 in its autoinhibited form. We find that the pseudokinase and kinase interact near the kinase active site and that most reported mutations in cancer-associated JAK alleles cluster in or near this interface. Mutation of residues near the TYK2 interface that are analogous to those in cancer-associated JAK alleles, including the V617F and "exon 12" JAK2 mutations, results in increased kinase activity in vitro. These data indicate that JAK pseudokinases are autoinhibitory domains that hold the kinase domain inactive until receptor dimerization stimulates transition to an active state.

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Organizational Affiliation: 
• Departments of Structural Biology and [e-mail] [e-mail].
Departments of Structural Biology and.
Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA 94080.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 73.94 kDa 
• Atom Count: 4,396 
• Modeled Residue Count: 539 
• Deposited Residue Count: 645 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TYK2	A	645	Homo sapiens	Mutation(s): 1  Gene Names: TYK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P29597 (Homo sapiens) Explore P29597  Go to UniProtKB:  P29597
PHAROS:  P29597 GTEx:  ENSG00000105397

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2TT	B [auth A], C [auth A]	2-chloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide C16 H14 Cl N3 O2 BZYFIAMMQPKLOE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.257 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.015	α = 90
b = 111.015	β = 90
c = 123.955	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Eigenbrot, C., Ultsch, M., Wallweber, H.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description