7B2N | pdb_00007b2n

Crystal structure of Chlamydomonas reinhardtii chloroplastic Fructose bisphosphate aldolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 7B2N

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii.

Le Moigne, T.Sarti, E.Nourisson, A.Zaffagnini, M.Carbone, A.Lemaire, S.D.Henri, J.

(2022) J Struct Biol 214: 107873-107873

  • DOI: https://doi.org/10.1016/j.jsb.2022.107873
  • Primary Citation Related Structures: 
    7B2N

  • PubMed Abstract: 

    The Calvin-Benson cycle fixes carbon dioxide into organic triosephosphates through the collective action of eleven conserved enzymes. Regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco-mediated carboxylation, requires two lyase reactions catalyzed by fructose-1,6-bisphosphate aldolase (FBA). While cytoplasmic FBA has been extensively studied in non-photosynthetic organisms, functional and structural details are limited for chloroplast FBA encoded by oxygenic phototrophs. Here we determined the crystal structure of plastidial FBA from the unicellular green alga Chlamydomonas reinhardtii (Cr). We confirm that CrFBA folds as a TIM barrel, describe its catalytic pocket and homo-tetrameric state. Multiple sequence profiling classified the photosynthetic paralogs of FBA in a distinct group from non-photosynthetic paralogs. We mapped the sites of thiol- and phospho-based post-translational modifications known from photosynthetic organisms and predict their effects on enzyme catalysis.


  • Organizational Affiliation
    • Sorbonne Université, CNRS, UMR 7238, Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative, 4 place Jussieu, F-75005 Paris, France; Sorbonne Université, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, 13 rue Pierre et Marie Curie, 75005 Paris, France; Faculty of Sciences, Doctoral School of Plant Sciences, Université Paris-Saclay, 91190 Saint-Aubin, France.

Macromolecule Content 

  • Total Structure Weight: 318.37 kDa 
  • Atom Count: 21,458 
  • Modeled Residue Count: 2,649 
  • Deposited Residue Count: 2,872 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolase 1, chloroplastic
A, B, C, D, E
A, B, C, D, E, F, G, H
359Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: ALDCHLCHLREDRAFT_24459
EC: 4.1.2.13
UniProt
Find proteins for Q42690 (Chlamydomonas reinhardtii)
Explore Q42690 
Go to UniProtKB:  Q42690
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42690
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
AA [auth D]
BA [auth E]
CA [auth E]
DA [auth F]
EA [auth F]
AA [auth D],
BA [auth E],
CA [auth E],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth F],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
L [auth A],
LA [auth H],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
R [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.493α = 90
b = 251.068β = 90.11
c = 126.411γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceJCJC CALVINTERACT ANR-19-CE11-0009

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description