3TNQ

Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

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Literature

Structure and allostery of the PKA RIIbeta tetrameric holoenzyme

Zhang, P.Smith-Nguyen, E.V.Keshwani, M.M.Deal, M.S.Kornev, A.P.Taylor, S.S.

(2012) Science 335: 712-716

  • DOI: 10.1126/science.1213979
  • Primary Citation of Related Structures:  
    3TNP, 3TNQ

  • PubMed Abstract: 
  • In its physiological state, cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is a tetramer that contains a regulatory (R) subunit dimer and two catalytic (C) subunits. We describe here the 2.3 angstrom structure of full-length tetrameric RIIβ(2):C(2) holoenzyme ...

    In its physiological state, cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is a tetramer that contains a regulatory (R) subunit dimer and two catalytic (C) subunits. We describe here the 2.3 angstrom structure of full-length tetrameric RIIβ(2):C(2) holoenzyme. This structure showing a dimer of dimers provides a mechanistic understanding of allosteric activation by cAMP. The heterodimers are anchored together by an interface created by the β4-β5 loop in the RIIβ subunit, which docks onto the carboxyl-terminal tail of the adjacent C subunit, thereby forcing the C subunit into a fully closed conformation in the absence of nucleotide. Diffusion of magnesium adenosine triphosphate (ATP) into these crystals trapped not ATP, but the reaction products, adenosine diphosphate and the phosphorylated RIIβ subunit. This complex has implications for the dissociation-reassociation cycling of PKA. The quaternary structure of the RIIβ tetramer differs appreciably from our model of the RIα tetramer, confirming the small-angle x-ray scattering prediction that the structures of each PKA tetramer are different.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093-0654, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein kinase, cAMP-dependent, catalytic, alphaA [auth B]350Rattus norvegicusMutation(s): 0 
Gene Names: PrkacarCG_51506
EC: 2.7.11.11
UniProt
Find proteins for P27791 (Rattus norvegicus)
Explore P27791 
Go to UniProtKB:  P27791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27791
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase type II-beta regulatory subunitB [auth A]416Mus musculusMutation(s): 1 
Gene Names: Prkar2b
UniProt
Find proteins for P31324 (Mus musculus)
Explore P31324 
Go to UniProtKB:  P31324
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31324
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A [auth B]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth B]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.819α = 90
b = 212.753β = 90
c = 61.951γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references