3O7L | pdb_00003o7l

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

PDB DOI: https://doi.org/10.2210/pdb3O7L/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-30 Released: 2010-10-06
Deposition Author(s): Cheng, C.Y., Taylor, S.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.287 (Depositor)
R-Value Work:
0.216 (Depositor), 0.231 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 20890288 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.452
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 83.63 kDa
Atom Count: 5,231
Modeled Residue Count: 677
Deposited Residue Count: 715
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A [auth B]	350	Mus musculus	Mutation(s): 0 Gene Names: Pkaca, Prkaca EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus) Explore P05132 Go to UniProtKB: P05132
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05132
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	B [auth D]	350	Mus musculus	Mutation(s): 0 Gene Names: Pkaca, Prkaca EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus) Explore P05132 Go to UniProtKB: P05132
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05132
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cardiac phospholamban	C [auth I]	15	N/A	Mutation(s): 0
UniProt
Find proteins for P61014 (Mus musculus) Explore P61014 Go to UniProtKB: P61014
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61014
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A [auth B]	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR
SEP Query on SEP	B [auth D]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.287 (Depositor)
R-Value Work: 0.216 (Depositor), 0.231 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.193	α = 90
b = 92.193	β = 90
c = 192.186	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-10-06

Deposition Author(s):

Cheng, C.Y.

Taylor, S.S.

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
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary