1L3R

Crystal Structure of a Transition State Mimic of the Catalytic Subunit of cAMP-dependent Protein Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.

MadhusudanAkamine, P.Xuong, N.H.Taylor, S.S.

(2002) Nat.Struct.Mol.Biol. 9: 273-277

  • DOI: 10.1038/nsb780

  • PubMed Abstract: 
  • To understand the molecular mechanism underlying phosphoryl transfer of cAMP-dependent protein kinase, the structure of the catalytic subunit in complex with ADP, aluminum fluoride, Mg2+ ions and a substrate peptide was determined at 2.0 A resolution ...

    To understand the molecular mechanism underlying phosphoryl transfer of cAMP-dependent protein kinase, the structure of the catalytic subunit in complex with ADP, aluminum fluoride, Mg2+ ions and a substrate peptide was determined at 2.0 A resolution. Aluminum fluoride was modeled as AlF3 in a planar geometry; it is positioned 2.3 A from both the donor oxygen of ADP and the hydroxyl group of the recipient Ser residue. In this configuration, the aluminum atom forms a trigonal bipyramidal coordination with the oxygen atoms of the donor and recipient groups at the apical positions. This arrangement suggests that aluminum fluoride mimics the transition state and provides the first direct structural evidence for the in-line mechanism of phosphoryl transfer in a protein kinase.


    Related Citations: 
    • 2.0 A Refined Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with a Peptide Inhibitor and Detergent
      Knighton, D.R.,Bell, S.M.,Zheng, J.,Ten Eyck, L.F.,Xuong, N.,Taylor, S.S.,Sowadski, J.M.
      (1993) Acta Crystallogr.,Sect.D 49: 357
    • cAMP-dependent Protein Kinase: Crystallografic Insights into Substrate Recognition and Phosphotransfer
      Madhusudan,Trafny, E.A.,Xuong, N.H.,Adams, J.A.,Ten Eyck, L.F.,Taylor, S.S.,Sowadski, J.M.
      (1994) Protein Sci. 3: 176
    • 2.2 A Refined Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with MnATP and a Peptide Inhibitor
      Zheng, J.,Trafny, E.A.,Knighton, D.R.,Xuong, N.,Taylor, S.S.,Ten Eyck, L.F.,Sowadski, J.M.
      (1993) Acta Crystallogr.,Sect.D 49: 362


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093-0654, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT
E
350Mus musculusGene 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 INHIBITOR, MUSCLE/BRAIN FORM
I
20Rattus norvegicusGene Names: Pkia
Find proteins for P63249 (Rattus norvegicus)
Go to UniProtKB:  P63249
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
E
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
E
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
E
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.680α = 90.00
b = 75.700β = 90.00
c = 80.550γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance