4UT3 | pdb_00004ut3

X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide

• PDB DOI: https://doi.org/10.2210/pdb4UT3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2014-07-17 Released: 2015-07-22 
• Deposition Author(s): Zeh Silva, M., Kopec, J., Fotinou, D., Steiner, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Targeted Redox Inhibition of Protein Phosphatase 1 by Nox4 Regulates Eif2Alpha-Mediated Stress Signaling.

Santos, C.X., Hafstad, A.D., Beretta, M., Zhang, M., Molenaar, C., Kopec, J., Fotinou, D., Murray, T.V., Cobb, A.M., Martin, D., Zeh Silva, M., Anilkumar, N., Schroder, K., Shanahan, C.M., Brewer, A.C., Brandes, R.P., Blanc, E., Parsons, M., Belousov, V., Cammack, R., Hider, R.C., Steiner, R.A., Shah, A.M.

(2016) EMBO J 35: 319

• PubMed: 26742780 
• DOI: https://doi.org/10.15252/embj.201592394
• Primary Citation Related Structures: 
  4UT2, 4UT3


• PubMed Abstract: 
  

  Phosphorylation of translation initiation factor 2α (eIF2α) attenuates global protein synthesis but enhances translation of activating transcription factor 4 (ATF4) and is a crucial evolutionarily conserved adaptive pathway during cellular stresses. The serine-threonine protein phosphatase 1 (PP1) deactivates this pathway whereas prolonging eIF2α phosphorylation enhances cell survival. Here, we show that the reactive oxygen species-generating NADPH oxidase-4 (Nox4) is induced downstream of ATF4, binds to a PP1-targeting subunit GADD34 at the endoplasmic reticulum, and inhibits PP1 activity to increase eIF2α phosphorylation and ATF4 levels. Other PP1 targets distant from the endoplasmic reticulum are unaffected, indicating a spatially confined inhibition of the phosphatase. PP1 inhibition involves metal center oxidation rather than the thiol oxidation that underlies redox inhibition of protein tyrosine phosphatases. We show that this Nox4-regulated pathway robustly enhances cell survival and has a physiologic role in heart ischemia-reperfusion and acute kidney injury. This work uncovers a novel redox signaling pathway, involving Nox4-GADD34 interaction and a targeted oxidative inactivation of the PP1 metal center, that sustains eIF2α phosphorylation to protect tissues under stress.

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Organizational Affiliation: 
• Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK.
Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK Cardiovascular Research Group, Department of Medical Biology, The Arctic University of Norway, Tromsø, Norway.
Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK.
Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany.
MRC Centre for Developmental Neurobiology, King's College London, London, UK.
Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
Institute of Pharmaceutical Science, King's College London, London, UK.
Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.52 kDa 
• Atom Count: 4,936 
• Modeled Residue Count: 588 
• Deposited Residue Count: 646 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT	A	323	Homo sapiens	Mutation(s): 0  EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P36873 (Homo sapiens) Explore P36873  Go to UniProtKB:  P36873
PHAROS:  P36873 GTEx:  ENSG00000186298

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT	B	323	Homo sapiens	Mutation(s): 0  EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P36873 (Homo sapiens) Explore P36873  Go to UniProtKB:  P36873
PHAROS:  P36873 GTEx:  ENSG00000186298

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.45	α = 90
b = 105.22	β = 90.34
c = 89.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Zeh Silva, M., Kopec, J., Fotinou, D., Steiner, R.A.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary