9QM7 | pdb_00009qm7

Crystal structure of S-nitrosylated triose phosphate isomerase from Chlamydomonas reinhardtii

• PDB DOI: https://doi.org/10.2210/pdb9QM7/pdb

• Classification: ISOMERASE
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-21 Released: 2025-10-01 
• Deposition Author(s): Fanti, S., Fermani, S., Gabellini, G., Zaffagnini, M., Meloni, M., Peppi, G.M.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Molecular and structural basis for nitrosoglutathione-dependent redox regulation of triosephosphate isomerase from Chlamydomonas reinhardtii.

Meloni, M., Mattioli, E.J., Fanti, S., Peppi, G.M.E., Bin, T., Gabellini, G., Tedesco, D., Henri, J., Trost, P., Lemaire, S.D., Calvaresi, M., Fermani, S., Zaffagnini, M.

(2025) Plant Sci 362: 112768-112768

• PubMed: 40946919 
• DOI: https://doi.org/10.1016/j.plantsci.2025.112768
• Primary Citation of Related Structures:  
  9QM7, 9R6M


• PubMed Abstract: 
  

  Protein S-nitrosylation is a reversible redox-based post-translational modification that plays an important role in cell signaling by modulating protein function and stability. At the molecular level, S-nitrosylation consists of the formation of a nitrosothiol (-SNO) and is primarily induced by the trans-nitrosylating agent nitrosoglutathione (GSNO). Triosephosphate isomerase (TPI), which catalyzes the interconversion of dihydroxyacetone phosphate and glyceraldehyde-3-phosphate, has been identified as a putative target of S-nitrosylation in both plant and non-plant systems. Here we investigate the molecular basis for GSNO-dependent regulation of chloroplast TPI from the model green alga Chlamydomonas reinhardtii (CrTPI). Molecular modelling identified Cys14 and Cys219 as potential sites for interaction with GSNO, though crystallography of GSNO-treated CrTPI revealed S-nitrosylation only at Cys14. To disclose GSNO target sites, we generated and characterized Cys-to-Ser variants for Cys14 and Cys219, identifying Cys219 as a key residue mediating the GSNO-dependent modulation of CrTPI activity. Molecular dynamics simulations further revealed the stabilizing interactions of S-nitrosylated cysteines with their local environments. Overall, our results indicate that CrTPI catalysis is modulated by GSNO through a redox-based mechanism involving Cys219, which highlights a conserved regulatory strategy shared with human TPI.

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Organizational Affiliation: 
• Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 42, Bologna I-40126, Italy.
Department of Chemistry 'G. Ciamician', University of Bologna, via Selmi 2, Bologna I-40126, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, Preclinical & Translational Research in Oncology lab (PRO), Italy.
Department of Chemistry 'G. Ciamician', University of Bologna, via Selmi 2, Bologna I-40126, Italy.
Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Bologna I-40129, Italy.
Sorbonne Université, CNRS, Department of Computational, Quantitative and Synthetic Biology, Paris F-75005, France; Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, Paris F-75005, France.
Sorbonne Université, CNRS, Department of Computational, Quantitative and Synthetic Biology, Paris F-75005, France; Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, Paris F-75005, France; Sorbonne Université, Université de Technologie de Compiègne, CNRS, INSERM, Biofoundry Alliance Sorbonne Université, Paris F-75005, France.
Department of Chemistry 'G. Ciamician', University of Bologna, via Selmi 2, Bologna I-40126, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, Preclinical & Translational Research in Oncology lab (PRO), Italy. Electronic address: [e-mail].
Department of Chemistry 'G. Ciamician', University of Bologna, via Selmi 2, Bologna I-40126, Italy; Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, Bologna 40064, Italy. Electronic address: [e-mail].
Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 42, Bologna I-40126, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 27.59 kDa 
• Atom Count: 2,368 
• Modeled Residue Count: 252 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloroplast triosephosphate isomerase	A	255	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: TIM, CHLRE_01g029300v5
UniProt
Find proteins for Q5S7Y5 (Chlamydomonas reinhardtii) Explore Q5S7Y5  Go to UniProtKB:  Q5S7Y5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MPD	B [auth A], C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC	A	L-PEPTIDE LINKING	C3 H6 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.893	α = 90
b = 93.361	β = 90
c = 100.499	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Fanti, S., Fermani, S., Gabellini, G., Zaffagnini, M., Meloni, M., Peppi, G.M.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release