6ZK6 | pdb_00006zk6

Protein Phosphatase 1 (PP1) T320E mutant

• PDB DOI: https://doi.org/10.2210/pdb6ZK6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-06-29 Released: 2020-11-18 
• Deposition Author(s): Salvi, F., Barabas, O., Koehn, M.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Towards Dissecting the Mechanism of Protein Phosphatase-1 Inhibition by Its C-Terminal Phosphorylation.

Salvi, F., Hoermann, B., Del Pino Garcia, J., Fontanillo, M., Derua, R., Beullens, M., Bollen, M., Barabas, O., Kohn, M.

(2021) Chembiochem 22: 834-838

• PubMed: 33085143 
• DOI: https://doi.org/10.1002/cbic.202000669
• Primary Citation Related Structures: 
  6ZK6


• PubMed Abstract: 
  

  Phosphoprotein phosphatase-1 (PP1) is a key player in the regulation of phospho-serine (pSer) and phospho-threonine (pThr) dephosphorylation and is involved in a large fraction of cellular signaling pathways. Aberrant activity of PP1 has been linked to many diseases, including cancer and heart failure. Besides a well-established activity control by regulatory proteins, an inhibitory function for phosphorylation (p) of a Thr residue in the C-terminal intrinsically disordered tail of PP1 has been demonstrated. The associated phenotype of cell-cycle arrest was repeatedly proposed to be due to autoinhibition of PP1 through either conformational changes or substrate competition. Here, we use PP1 variants created by mutations and protein semisynthesis to differentiate between these hypotheses. Our data support the hypothesis that pThr exerts its inhibitory function by mediating protein complex formation rather than by a direct mechanism of structural changes or substrate competition.

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Organizational Affiliation: 
• Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.
Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany.
Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany.
Laboratory of Biosignaling and Therapeutics Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
Laboratory of Protein Phosphorylation and Proteomics Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
SyBioMa, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.01 kDa 
• Atom Count: 2,434 
• Modeled Residue Count: 291 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	A	331	Homo sapiens	Mutation(s): 1  Gene Names: PPP1CA, PPP1A EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens) Explore P62136  Go to UniProtKB:  P62136
PHAROS:  P62136 GTEx:  ENSG00000172531

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	D [auth A], E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.546	α = 90
b = 68.749	β = 90
c = 127.846	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Salvi, F., Barabas, O., Koehn, M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	336567

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary