6BHC

Crystal structure of pseduokinase PEAK1 (Sugen Kinase 269)

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2017-10-30 Released: 2017-12-13 
  • Deposition Author(s): Ha, B.H., Boggon, T.J.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The crystal structure of pseudokinase PEAK1 (Sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization.

Ha, B.H.Boggon, T.J.

(2018) J Biol Chem 293: 1642-1650

  • DOI: 10.1074/jbc.RA117.000751
  • Primary Citation of Related Structures:  
    6BHC

  • PubMed Abstract: 
  • The pseudokinase group encompasses some 10% of protein kinases, but pseudokinases diverge from canonical kinases in key motifs. The two members of the small new kinase family 3 (NKF3) group are considered pseudokinases. These proteins, pseudopodium-e ...

    The pseudokinase group encompasses some 10% of protein kinases, but pseudokinases diverge from canonical kinases in key motifs. The two members of the small new kinase family 3 (NKF3) group are considered pseudokinases. These proteins, pseudopodium-enriched atypical kinase 1 (PEAK1, Sugen kinase 269, or SgK269) and pragmin (Sugen kinase 223 or SgK223), act as scaffolds in growth factor signaling pathways, and both contain a kinase fold with degraded kinase motifs at their C termini. These kinases may harbor regions that mediate oligomerization or control other aspects of signal transduction, but a lack of structural information has precluded detailed investigations into their functional roles. In this study, we determined the X-ray crystal structure of the PEAK1 pseudokinase domain to 2.3 Å resolution. The structure revealed that the PEAK1 kinase-like domain contains a closed nucleotide-binding cleft that in this conformation may deleteriously affect nucleotide binding. Moreover, we found that N- and C-terminal extensions create a highly unusual all α-helical split-dimerization region, termed here the split helical dimerization (SHED) region. Sequence conservation analysis suggested that this region facilitates a dimerization mode that is conserved between PEAK1 and pragmin. Finally, we observed structural similarities between the PEAK1 SHED region and the C-terminal extension of the Parkinson's disease-associated kinase PINK1. In summary, PEAK1's kinase cleft is occluded, and its newly identified SHED region may promote an unexpected dimerization mode. Similarities of PEAK1 with the active kinase PINK1 may reclassify the latter as a member of the new kinase family 3 group.


    Organizational Affiliation

    Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pseudopodium-enriched atypical kinase 1A438Homo sapiensMutation(s): 1 
Gene Names: PEAK1KIAA2002
EC: 2.7.10.2
Find proteins for Q9H792 (Homo sapiens)
Explore Q9H792 
Go to UniProtKB:  Q9H792
NIH Common Fund Data Resources
PHAROS  Q9H792
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 2 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/514 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.923α = 90
b = 72.724β = 90
c = 103.192γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-30 
  • Released Date: 2017-12-13 
  • Deposition Author(s): Ha, B.H., Boggon, T.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS085078
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM109487
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM114621
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM102262

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.3: 2018-02-14
    Changes: Database references
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence