6PQ1

Structure of the Fremyella diplosiphon OCP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix.

Kuznetsova, V.Dominguez-Martin, M.A.Bao, H.Gupta, S.Sutter, M.Kloz, M.Rebarz, M.Precek, M.Chen, Y.Petzold, C.J.Ralston, C.Y.Kerfeld, C.A.Polivka, T.

(2020) Biochim Biophys Acta Bioenerg 1861: 148120-148120

  • DOI: https://doi.org/10.1016/j.bbabio.2019.148120
  • Primary Citation of Related Structures:  
    6PQ1

  • PubMed Abstract: 

    The orange carotenoid protein (OCP) is a structurally and functionally modular photoactive protein involved in cyanobacterial photoprotection. Recently, based on bioinformatic analysis and phylogenetic relationships, new families of OCP have been described, OCP2 and OCPx. The first characterization of the OCP2 showed both faster photoconversion and back-conversion, and lower fluorescence quenching of phycobilisomes relative to the well-characterized OCP1. Moreover, OCP2 is not regulated by the fluorescence recovery protein (FRP). In this work, we present a comprehensive study combining ultrafast spectroscopy and structural analysis to compare the photoactivation mechanisms of OCP1 and OCP2 from Tolypothrix PCC 7601. We show that despite significant differences in their functional characteristics, the spectroscopic properties of OCP1 and OCP2 are comparable. This indicates that the OCP functionality is not directly related to the spectroscopic properties of the bound carotenoid. In addition, the structural analysis by X-ray footprinting reveals that, overall, OCP1 and OCP2 have grossly the same photoactivation mechanism. However, the OCP2 is less reactive to radiolytic labeling, suggesting that the protein is less flexible than OCP1. This observation could explain fast photoconversion of OCP2.


  • Organizational Affiliation

    Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orange carotenoid-binding protein326Tolypothrix sp. PCC 7601Mutation(s): 0 
Gene Names: FDUTEX481_08602
UniProt
Find proteins for A0A0D6KM24 (Tolypothrix sp. PCC 7601)
Explore A0A0D6KM24 
Go to UniProtKB:  A0A0D6KM24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D6KM24
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
45D (Subject of Investigation/LOI)
Query on 45D

Download Ideal Coordinates CCD File 
B [auth A]beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.019α = 90
b = 95.019β = 90
c = 78.523γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description