7ZQK

Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) complexed with NAD+

Summary for 7ZQK

• Entry DOI: 10.2210/pdb7zqk/pdb
• Related: 7ZQ3 7ZQ4
• Descriptor: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: oxidoreductase, rossman-fold domain, calvin-benson cycle, pyridin dinucleotide cofactors
• Biological source: Chlamydomonas reinhardtii
• Total number of polymer chains: 2
• Total formula weight: 77946.56

Authors

Fermani, S.,Zaffagnini, M.,Lemaire, S.D.,Falini, G.,Fanti, S.,Rossi, J. (deposition date: 2022-04-30, release date: 2022-07-20, Last modification date: 2024-01-31)

Primary citation

Mattioli, E.J.,Rossi, J.,Meloni, M.,De Mia, M.,Marchand, C.H.,Tagliani, A.,Fanti, S.,Falini, G.,Trost, P.,Lemaire, S.D.,Fermani, S.,Calvaresi, M.,Zaffagnini, M.
Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH.
Redox Biol, 54:102387-102387, 2022

PubMed Abstract: S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes reversible enzyme inhibition by inducing S-nitrosylation. While the cofactor NADP partially protects the enzyme from GSNO-mediated S-nitrosylation, protein inhibition is not observed in the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible for CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP and NAD reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. The reaction mechanism of GSNO with CrGAPA Cys149 was investigated by quantum mechanical/molecular mechanical calculations, which permitted to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.

PubMed: 35793584
DOI: 10.1016/j.redox.2022.102387

Experimental method

X-RAY DIFFRACTION (2.2 Å)