1JLU

Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with a Phosphorylated Substrate Peptide and Detergent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.

MadhusudanTrafny, E.A.Xuong, N.H.Adams, J.A.Ten Eyck, L.F.Taylor, S.S.Sowadski, J.M.

(1994) Protein Sci 3: 176-187

  • DOI: 10.1002/pro.5560030203
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of ternary and binary substrate complexes of the catalytic subunit of cAMP-dependent protein kinase has been refined at 2.2 and 2.25 A resolution, respectively. The ternary complex contains ADP and a 20-residue substrate peptide ...

    The crystal structure of ternary and binary substrate complexes of the catalytic subunit of cAMP-dependent protein kinase has been refined at 2.2 and 2.25 A resolution, respectively. The ternary complex contains ADP and a 20-residue substrate peptide, whereas the binary complex contains the phosphorylated substrate peptide. These 2 structures were refined to crystallographic R-factors of 17.5 and 18.1%, respectively. In the ternary complex, the hydroxyl oxygen OG of the serine at the P-site is 2.7 A from the OD1 atom of Asp 166. This is the first crystallographic evidence showing the direct interaction of this invariant carboxylate with a peptide substrate, and supports the predicted role of Asp 166 as a catalytic base and as an agent to position the serine -OH for nucleophilic attack. A comparison of the substrate and inhibitor ternary complexes places the hydroxyl oxygen of the serine 2.7 A from the gamma-phosphate of ATP and supports a direct in-line mechanism for phosphotransfer. In the binary complex, the phosphate on the Ser interacts directly with the epsilon N of Lys 168, another conserved residue. In the ternary complex containing ATP and the inhibitor peptide, Lys 168 interacts electrostatically with the gamma-phosphate of ATP (Zheng J, Knighton DR, Ten Eyck LF, Karlsson R, Xuong NH, Taylor SS, Sowadski JM, 1993, Biochemistry 32:2154-2161). Thus, Lys 168 remains closely associated with the phosphate in both complexes. A comparison of this binary complex structure with the recently solved structure of the ternary complex containing ATP and inhibitor peptide also reveals that the phosphate atom traverses a distance of about 1.5 A following nucleophilic attack by serine and transfer to the peptide. No major conformational changes of active site residues are seen when the substrate and product complexes are compared, although the binary complex with the phosphopeptide reveals localized changes in conformation in the region corresponding to the glycine-rich loop. The high B-factors for this loop support the conclusion that this structural motif is a highly mobile segment of the protein.


    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

    Organizational Affiliation

    Department of Medicine, University of California at San Diego, La Jolla 92093-0654.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNITE350Mus musculusMutation(s): 0 
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 LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN FORMS20N/AMutation(s): 2 
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
NIH Common Fund Data Resources
PHAROS  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

Download CCD File 
E
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
EL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
EL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.87α = 90
b = 75.58β = 90
c = 80.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description