3O7L

Crystal Structure of phospholamban (1-19):PKA C-subunit:AMP-PNP:Mg2+ complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dynamics connect substrate recognition to catalysis in protein kinase A.

Masterson, L.R.Cheng, C.Yu, T.Tonelli, M.Kornev, A.Taylor, S.S.Veglia, G.

(2010) Nat.Chem.Biol. 6: 821-828

  • DOI: 10.1038/nchembio.452

  • PubMed Abstract: 
  • Atomic resolution studies of protein kinases have traditionally been carried out in the inhibitory state, limiting our current knowledge on the mechanisms of substrate recognition and catalysis. Using NMR, X-ray crystallography and thermodynamic meas ...

    Atomic resolution studies of protein kinases have traditionally been carried out in the inhibitory state, limiting our current knowledge on the mechanisms of substrate recognition and catalysis. Using NMR, X-ray crystallography and thermodynamic measurements, we analyzed the substrate recognition process of cAMP-dependent protein kinase (PKA), finding that entropy and protein dynamics play a prominent role. The nucleotide acts as a dynamic and allosteric activator by coupling the two lobes of apo PKA, enhancing the enzyme dynamics synchronously and priming it for catalysis. The formation of the ternary complex is entropically driven, and NMR spin relaxation data reveal that both substrate and PKA are dynamic in the closed state. Our results show that the enzyme toggles between open and closed states, which indicates that a conformational selection rather than an induced-fit mechanism governs substrate recognition.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
B
350Mus musculusMutation(s): 0 
Gene Names: Prkaca (Pkaca)
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Go to UniProtKB:  P05132
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
D
350Mus musculusMutation(s): 0 
Gene Names: Prkaca (Pkaca)
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Go to UniProtKB:  P05132
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cardiac phospholamban
I
15Mus musculusMutation(s): 0 
Gene Names: Pln
Find proteins for P61014 (Mus musculus)
Go to UniProtKB:  P61014
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
B, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.216 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 92.193α = 90.00
b = 92.193β = 90.00
c = 192.186γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling
PHASESphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance