8S59

Cryo-EM structure of the active dodecameric Methanosarcina mazei glutamine synthetase.

This is a non-PDB format compatible entry.

Summary for 8S59

• Entry DOI: 10.2210/pdb8s59/pdb
• EMDB information: 19730
• Descriptor: Glutamine synthetase, 2-OXOGLUTARIC ACID (3 entities in total)
• Functional Keywords: glutamine synthetases, nitrogen metabolism, ammonium assimilation, cryo-em, cytosolic protein
• Biological source: Methanosarcina mazei Go1
• Total number of polymer chains: 12
• Total formula weight: 608057.63

Authors

Kumar, A.,Schuller, J.M.,Schmitz, R.A. (deposition date: 2024-02-23, release date: 2025-01-08, Last modification date: 2025-05-14)

Primary citation

Herdering, E.,Reif-Trauttmansdorff, T.,Kumar, A.,Habenicht, T.,Hochberg, G.,Bohn, S.,Schuller, J.,Schmitz, R.A.
2-oxoglutarate triggers assembly of active dodecameric Methanosarcina mazei glutamine synthetase.
Elife, 13:-, 2025

PubMed Abstract: Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP-dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeon , it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK and sP26) has been reported. Here, we show that the strong activation of GS (GlnA) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on the binding of glutamine to the catalytic site. Based on our findings, we propose that under nitrogen limitation the induction of GS into a catalytically active dodecamer is not affected by GlnK and crucially depends on the presence of 2-OG.

PubMed: 40163028
DOI: 10.7554/eLife.97484

Experimental method

ELECTRON MICROSCOPY (2.39 Å)