3O7L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.216 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    3O7L

  • 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 measurements, we analyzed the substrate recognition process of cAMP-dependent protein kinase (PKA), finding that entropy and protein dynamics play a prominent role ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA [auth B]350Mus musculusMutation(s): 0 
Gene Names: PkacaPrkaca
EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus)
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Go to UniProtKB:  P05132
Entity Groups  
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UniProt GroupP05132
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaB [auth D]350Mus musculusMutation(s): 0 
Gene Names: PkacaPrkaca
EC: 2.7.11.11
UniProt
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Go to UniProtKB:  P05132
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UniProt GroupP05132
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cardiac phospholambanC [auth I]15N/AMutation(s): 0 
UniProt
Find proteins for P61014 (Mus musculus)
Explore P61014 
Go to UniProtKB:  P61014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61014
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
G [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.193α = 90
b = 92.193β = 90
c = 192.186γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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