4LOW

Structure and identification of a pterin dehydratase-like protein as a RuBisCO assembly factor in the alpha-carboxysome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 1.3 of the entry. See complete history


Literature

Structure and Identification of a Pterin Dehydratase-like Protein as a Ribulose-bisphosphate Carboxylase/Oxygenase (RuBisCO) Assembly Factor in the alpha-Carboxysome.

Wheatley, N.M.Sundberg, C.D.Gidaniyan, S.D.Cascio, D.Yeates, T.O.

(2014) J Biol Chem 289: 7973-7981

  • DOI: 10.1074/jbc.M113.531236
  • Primary Citation of Related Structures:  
    4LOW

  • PubMed Abstract: 
  • Carboxysomes are proteinaceous bacterial microcompartments that increase the efficiency of the rate-limiting step in carbon fixation by sequestering reaction substrates. Typically, α-carboxysomes are genetically encoded as a single operon expressing the structural proteins and the encapsulated enzymes of the microcompartment ...

    Carboxysomes are proteinaceous bacterial microcompartments that increase the efficiency of the rate-limiting step in carbon fixation by sequestering reaction substrates. Typically, α-carboxysomes are genetically encoded as a single operon expressing the structural proteins and the encapsulated enzymes of the microcompartment. In addition, depending on phylogeny, as many as 13 other genes are found to co-occur near or within α-carboxysome operons. One of these genes codes for a protein with distant homology to pterin-4α-carbinolamine dehydratase (PCD) enzymes. It is present in all α-carboxysome containing bacteria and has homologs in algae and higher plants. Canonical PCDs play an important role in amino acid hydroxylation, a reaction not associated with carbon fixation. We determined the crystal structure of an α-carboxysome PCD-like protein from the chemoautotrophic bacterium Thiomonas intermedia K12, at 1.3-Å resolution. The protein retains a three-dimensional fold similar to canonical PCDs, although the prominent active site cleft present in PCD enzymes is disrupted in the α-carboxysome PCD-like protein. Using a cell-based complementation assay, we tested the PCD-like proteins from T. intermedia and two additional bacteria, and found no evidence for PCD enzymatic activity. However, we discovered that heterologous co-expression of the PCD-like protein from Halothiobacillus neapolitanus with RuBisCO and GroELS in Escherichia coli increased the amount of soluble, assembled RuBisCO recovered from cell lysates compared with co-expression of RuBisCO with GroELS alone. We conclude that this conserved PCD-like protein, renamed here α-carboxysome RuBisCO assembly factor (or acRAF), is a novel RuBisCO chaperone integral to α-carboxysome function.


    Organizational Affiliation

    From the Molecular Biology Interdepartmental Ph.D. Program and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
acRAFA, B89Thiomonas intermedia K12Mutation(s): 0 
Gene Names: Tint_0125
EC: 4.2.1.96
Find proteins for D5X340 (Thiomonas intermedia (strain K12))
Explore D5X340 
Go to UniProtKB:  D5X340
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.11α = 90
b = 51.11β = 90
c = 60.88γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXEmodel building
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Structure summary
  • Version 1.2: 2014-04-02
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description