6AE9

X-ray structure of the photosystem II phosphatase PBCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insights into Substrate Selectivity, Catalytic Mechanism, and Redox Regulation of Rice Photosystem II Core Phosphatase.

Liu, X.Chai, J.Ou, X.Li, M.Liu, Z.

(2019) Mol Plant 12: 86-98

  • DOI: https://doi.org/10.1016/j.molp.2018.11.006
  • Primary Citation of Related Structures:  
    6AE9

  • PubMed Abstract: 

    Photosystem II (PSII) core phosphatase (PBCP) selectively dephosphorylates PSII core proteins including D1, D2, CP43, and PsbH. PBCP function is required for efficient degradation of the D1 protein in the repair cycle of PSII, a supramolecular machinery highly susceptible to photodamage during oxygenic photosynthesis. Here we present structural and functional studies of PBCP from Oryza sativa (OsPBCP). In a symmetrical homodimer of OsPBCP, each monomer contains a PP2C-type phosphatase core domain, a large motif characteristic of PBCPs, and two small motifs around the active site. The large motif contributes to the formation of a substrate-binding surface groove, and is crucial for the selectivity of PBCP toward PSII core proteins and against the light-harvesting proteins. Remarkably, the phosphatase activity of OsPBCP is strongly inhibited by glutathione and H 2 O 2 . S-Glutathionylation of cysteine residues may introduce steric hindrance and allosteric effects to the active site. Collectively, these results provide detailed mechanistic insights into the substrate selectivity, redox regulation, and catalytic mechanism of PBCP.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable protein phosphatase 2C 1
A, B
260Oryza sativa Japonica GroupMutation(s): 1 
Gene Names: Os01g0164600LOC_Os01g07090B1189A09.48OsJ_000491P0701D05.3
EC: 3.1.3.16
UniProt
Find proteins for Q942P9 (Oryza sativa subsp. japonica)
Explore Q942P9 
Go to UniProtKB:  Q942P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ942P9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POG
Query on POG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
N [auth B]
(20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL
C21 H44 O8
OWRNLGZKEZSHGO-QAWAPDBNSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCY
Query on OCY
A, B
L-PEPTIDE LINKINGC5 H11 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.407α = 90
b = 166.407β = 90
c = 46.983γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
ARP/wARPmodel building
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB08020302
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31670749

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary