Crystal structure of CbbY (AT3G48420) from Arabidobsis thaliana

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

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Degradation of potent Rubisco inhibitor by selective sugar phosphatase.

Bracher, A.Sharma, A.Starling-Windhof, A.Hartl, F.U.Hayer-Hartl, M.

(2015) Nat Plants 1: 14002-14002

  • DOI: https://doi.org/10.1038/nplants.2014.2
  • Primary Citation of Related Structures:  
    4UAR, 4UAS, 4UAT, 4UAU, 4UAV

  • PubMed Abstract: 

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the conversion of atmospheric carbon dioxide into organic compounds in photosynthetic organisms. Alongside carboxylating the five-carbon sugar ribulose-1,5-bisphosphate (RuBP)(1-3), Rubisco produces a small amount of xylulose-1,5-bisphosphate (XuBP), a potent inhibitor of Rubisco(4). The AAA+ protein Rubisco activase removes XuBP from the active site of Rubisco in an ATP-dependent process(5,6). However, free XuBP rapidly rebinds to Rubisco, perpetuating its inhibitory effect. Here, we combine biochemical and structural analyses to show that the CbbY protein of the photosynthetic bacterium Rhodobacter sphaeroides and Arabidopsis thaliana is a highly selective XuBP phosphatase. We also show that CbbY converts XuBP to the non-inhibitory compound xylulose-5-phosphate, which is recycled back to RuBP. We solve the crystal structures of CbbY from R. sphaeroides and A. thaliana, and through mutational analysis show that the cap domain of the protein confers the selectivity for XuBP over RuBP. Finally, in vitro experiments with CbbY from R. sphaeroides reveal that CbbY cooperates with Rubisco activase to prevent a detrimental build-up of XuBP at the Rubisco active site. We suggest that CbbY, which is conserved in algae and plants, is an important component of the cellular machinery that has evolved to deal with the shortcomings of the ancient enzyme Rubisco.

  • Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloacid dehalogenase-like hydrolase domain-containing protein At3g48420246Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g48420T29H11.60CBBY
EC: 3.1.3
Find proteins for Q94K71 (Arabidopsis thaliana)
Explore Q94K71 
Go to UniProtKB:  Q94K71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94K71
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.725α = 90
b = 140.041β = 90
c = 87.107γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references