6G0I

Active Fe-PP1

• PDB DOI: https://doi.org/10.2210/pdb6G0I/pdb

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


• Deposited: 2018-03-18 Released: 2018-11-21 
• Deposition Author(s): Salvi, F., Barabas, O., Koehn, M.
• Funding Organization(s): ERC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Effects of stably incorporated iron on protein phosphatase-1 structure and activity.

Salvi, F., Trebacz, M., Kokot, T., Hoermann, B., Rios, P., Barabas, O., Koehn, M.

(2018) FEBS Lett 592: 4028-4038

• PubMed: 30403291 
• DOI: https://doi.org/10.1002/1873-3468.13284
• Primary Citation of Related Structures:  
  6G0I, 6G0J


• PubMed Abstract: 
  

  Protein phosphatase-1 (PP1) drives a large amount of phosphoSer/Thr protein dephosphorylations in eukaryotes to counteract multiple kinases in signaling pathways. The phosphatase requires divalent metal cations for catalytic activity and contains iron naturally. Iron has been suggested to have an influence on PP1 activity through Fe ²⁺ and Fe ³⁺ oxidation states. However, much biochemical and all structural data have been obtained with recombinant PP1 containing Mn ²⁺ ions. Purifying iron-containing PP1 from Escherichia coli has thus far not been possible. Here, we present the preparation, characterization, and structure of iron-bound PP1α in inactive and active states. We establish a key role for the electronic/redox properties of iron in PP1 activity and shed light on the difference in substrate specificity between iron- and manganese-containing PP1.

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Organizational Affiliation: 

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.96 kDa 
• Atom Count: 2,378 
• Modelled Residue Count: 286 
• 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): 0  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 (Subject of Investigation/LOI)	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE (Subject of Investigation/LOI)	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	E [auth A], F [auth A]	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: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.365	α = 90
b = 68.686	β = 90
c = 126.995	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Salvi, F., Barabas, O., Koehn, M.

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Funding Organization	Location	Grant Number
ERC	Germany	336567

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-01-02
  Changes: Data collection, Database references
• Version 1.2: 2019-01-09
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary