5B3F

Crystal structure of phosphoribulokinase from Methanospirillum hungatei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

Kono, T.Mehrotra, S.Endo, C.Kizu, N.Matusda, M.Kimura, H.Mizohata, E.Inoue, T.Hasunuma, T.Yokota, A.Matsumura, H.Ashida, H.

(2017) Nat Commun 8: 14007-14007

  • DOI: https://doi.org/10.1038/ncomms14007
  • Primary Citation of Related Structures:  
    5B3F

  • PubMed Abstract: 

    Two enzymes are considered to be unique to the photosynthetic Calvin-Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO 2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term 'reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin-Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO 2 as carbon source) remains unknown.


  • Organizational Affiliation

    Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribulokinase/uridine kinase
A, B
343Methanospirillum hungatei JF-1Mutation(s): 0 
Gene Names: Mhun_0794
UniProt
Find proteins for Q2FUB5 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FUB5 
Go to UniProtKB:  Q2FUB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FUB5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.414α = 90
b = 93.822β = 90
c = 99.942γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection