8A0H

Crystal structure of the E25A mutant of the Orange Carotenoid Protein X from Gloeobacter kilaueensis JS1 complexed with echinenone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

A primordial Orange Carotenoid Protein: Structure, photoswitching activity and evolutionary aspects.

Slonimskiy, Y.B.Zupnik, A.O.Varfolomeeva, L.A.Boyko, K.M.Maksimov, E.G.Sluchanko, N.N.

(2022) Int J Biol Macromol 222: 167-180

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.09.131
  • Primary Citation of Related Structures:  
    8A0H

  • PubMed Abstract: 

    Cyanobacteria are photosynthesizing prokaryotes responsible for the Great Oxygenation Event on Earth ~2.5 Ga years ago. They use a specific photoprotective mechanism based on the 35-kDa photoactive Orange Carotenoid Protein (OCP), a promising target for developing novel optogenetic tools and for biomass engineering. The two-domain OCP presumably stems from domain fusion, yet the primitive thylakoid-less cyanobacteria Gloeobacter encodes a complete OCP. Its photosynthesis regulation lacks the so-called Fluorescence Recovery Protein (FRP), which in Synechocystis inhibits OCP-mediated phycobilisome fluorescence quenching, and Gloeobacter OCP belongs to the recently defined, heterogeneous clade OCPX (GlOCPX), the least characterized compared to OCP2 and especially OCP1 clades. Here, we describe the first crystal structure of OCPX, which explains unique functional adaptations of Gloeobacter OCPX compared to OCP1 from Synechocystis. We show that monomeric GlOCPX exploits a remarkable intramolecular locking mechanism stabilizing its dark-adapted state and exhibits drastically accelerated, less temperature-dependent recovery after photoactivation. While GlOCPX quenches Synechocystis phycobilisomes similar to Synechocystis OCP1, it evades interaction with and regulation by FRP from other species and likely uses alternative mechanisms for fluorescence recovery. This analysis of a primordial OCPX sheds light on its evolution, rationalizing renaming and subdivision of the OCPX clade into subclades - OCP3a, OCP3b, OCP3c.


  • Organizational Affiliation

    A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OCP N-terminal domain-containing protein325Gloeobacter kilaueensis JS1Mutation(s): 1 
Gene Names: GKIL_2275
UniProt
Find proteins for U5QHX0 (Gloeobacter kilaueensis (strain ATCC BAA-2537 / CCAP 1431/1 / ULC 316 / JS1))
Explore U5QHX0 
Go to UniProtKB:  U5QHX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5QHX0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.735α = 90
b = 61.366β = 90
c = 145.075γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-15-2021-1354
Russian Foundation for Basic ResearchRussian Federation20-54-12018
German Research Foundation (DFG)GermanyFR1276/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description