7A1D | pdb_00007a1d

Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation)

• PDB DOI: https://doi.org/10.2210/pdb7A1D/pdb
• EM Map EMD-11606: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-08-12 Released: 2021-06-09 
• Deposition Author(s): Lazaro, M., Melero, R., Huet, C., Lopez-Alonso, J.P., Delgado, S., Dodu, A., Bruch, E.M., Abriata, L.A., Alzari, P.M., Valle, M., Lisa, M.N.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme.

Lazaro, M., Melero, R., Huet, C., Lopez-Alonso, J.P., Delgado, S., Dodu, A., Bruch, E.M., Abriata, L.A., Alzari, P.M., Valle, M., Lisa, M.N.

(2021) Commun Biol 4: 684-684

• PubMed: 34083757 
• DOI: https://doi.org/10.1038/s42003-021-02222-x
• Primary Citation Related Structures: 
  7A1D, 7JSR


• PubMed Abstract: 
  

  Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs ₁₈₀ ) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs ₁₈₀ in bacterial physiology, the lack of structural data for these enzymes has limited the progress of functional studies. Here we show that the mycobacterial L-GDH ₁₈₀ (mL-GDH ₁₈₀ ) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH ₁₈₀ involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors for allosteric regulation. These findings uncover unique aspects of the structure-function relationship in the subfamily of L-GDHs.

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Organizational Affiliation: 
• Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, Derio, Spain.
Centro Nacional de Biotecnología, CNB-CSIC, Darwin 3, Madrid, Spain.
Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, 25 rue du Docteur Roux, Paris, France.
CH, DBV-Technologies, 177-181 Avenue Pierre Brossolette, 92120 Montrouge, France; EMB, Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, 25 rue du Docteur Roux, Paris, France.
Integrated Structural Biology Department, IGBMC, 1 Rue Laurent Fries, Illkirch, France.
Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, Derio, Spain. [e-mail].
Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, 25 rue du Docteur Roux, Paris, France. [e-mail].
Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, Rosario, Argentina. [e-mail].
Plataforma de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario, Argentina. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 705.37 kDa 
• Atom Count: 33,784 
• Modeled Residue Count: 4,356 
• Deposited Residue Count: 6,444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-specific glutamate dehydrogenase	A, B, C, D	1,611	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: gdh, MSMEG_4699, MSMEI_4582 EC: 1.4.1.2
UniProt
Find proteins for A0R1C2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1C2  Go to UniProtKB:  A0R1C2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Lazaro, M., Melero, R., Huet, C., Lopez-Alonso, J.P., Delgado, S., Dodu, A., Bruch, E.M., Abriata, L.A., Alzari, P.M., Valle, M., Lisa, M.N.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PGC2018-098996-B-100

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-07-10
  Changes: Data collection
• Version 2.0: 2025-05-14
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary