6ZXT | pdb_00006zxt

High resolution crystal structure of chloroplastic ribose-5-phosphate isomerase from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.176 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii -An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle.

Le Moigne, T.Crozet, P.Lemaire, S.D.Henri, J.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21207787
  • Primary Citation Related Structures: 
    6ZXT

  • PubMed Abstract: 

    The Calvin-Benson cycle is the key metabolic pathway of photosynthesis responsible for carbon fixation and relies on eleven conserved enzymes. Ribose-5-phosphate isomerase (RPI) isomerizes ribose-5-phosphate into ribulose-5-phosphate and contributes to the regeneration of the Rubisco substrate. Plant RPI is the target of diverse post-translational modifications including phosphorylation and thiol-based modifications to presumably adjust its activity to the photosynthetic electron flow. Here, we describe the first experimental structure of a photosynthetic RPI at 1.4 Å resolution. Our structure confirms the composition of the catalytic pocket of the enzyme. We describe the homo-dimeric state of the protein that we observed in the crystal and in solution. We also map the positions of previously reported post-translational modifications and propose mechanisms by which they may impact the catalytic parameters. The structural data will inform the biochemical modeling of photosynthesis.


  • Organizational Affiliation
    • Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, 75005 Paris, France.

Macromolecule Content 

  • Total Structure Weight: 55.99 kDa 
  • Atom Count: 4,206 
  • Modeled Residue Count: 474 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribose-5-phosphate isomerase
A, B
255Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RPI1CHLRE_03g187450v5CHLREDRAFT_55838
EC: 5.3.1.6
UniProt
Find proteins for A8IRQ1 (Chlamydomonas reinhardtii)
Explore A8IRQ1 
Go to UniProtKB:  A8IRQ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8IRQ1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.176 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.152α = 90
b = 63.952β = 96.13
c = 80.909γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description