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: 2.00 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 Biol 9: 273-277

  • DOI: 10.1038/nsb780
  • Primary Citation of Related Structures:  
    1L3R

  • 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. Aluminum fluoride was modeled as AlF3 in a planar geometry; it is positioned 2 ...

    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 D Biol Crystallogr 49: 357
    • 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 D Biol Crystallogr 49: 362
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNITA [auth E]350Mus musculusMutation(s): 4 
Gene Names: PrkacaPkaca
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
Find proteins for P05132 (Mus musculus)
Explore P05132 
Go to UniProtKB:  P05132
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN FORMB [auth I]20N/AMutation(s): 2 
Find proteins for P63249 (Rattus norvegicus)
Explore P63249 
Go to UniProtKB:  P63249
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
EADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MPD
Query on MPD

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

Download Ideal Coordinates CCD File 
F [auth E]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.68α = 90
b = 75.7β = 90
c = 80.55γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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