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- PDB-7a1d: Cryo-EM map of the large glutamate dehydrogenase composed of 180 ... -

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Basic information

Entry
Database: PDB / ID: 7a1d
TitleCryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation)
ComponentsNAD-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / large glutamate dehydrogenase Mycobacterium metabolism
Function / homologyNAD-glutamate dehydrogenase, bacteria / NAD-glutamate dehydrogenase / Bacterial NAD-glutamate dehydrogenase, catalytic domain / glutamate dehydrogenase / glutamate catabolic process to 2-oxoglutarate / glutamate dehydrogenase (NAD+) activity / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily / NAD-specific glutamate dehydrogenase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsLazaro, 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 support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098996-B-100 Spain
CitationJournal: Commun Biol / Year: 2021
Title: 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme.
Authors: Melisa Lázaro / Roberto Melero / Charlotte Huet / Jorge P López-Alonso / Sandra Delgado / Alexandra Dodu / Eduardo M Bruch / Luciano A Abriata / Pedro M Alzari / Mikel Valle / María-Natalia Lisa /
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) contain long N- ...Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs 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 (mL-GDH) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH 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.
History
DepositionAug 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / em_admin / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase
C: NAD-specific glutamate dehydrogenase
D: NAD-specific glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)705,3674
Polymers705,3674
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6930 Å2
ΔGint-29 kcal/mol
Surface area191610 Å2
MethodPISA

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Components

#1: Protein
NAD-specific glutamate dehydrogenase / NAD-GDH / NAD(+)-dependent glutamate dehydrogenase


Mass: 176341.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: gdh, MSMEG_4699, MSMEI_4582 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0R1C2, glutamate dehydrogenase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.705 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 6
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 47170 X / Calibrated defocus min: 670 nm / Calibrated defocus max: 3260 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14rc3_3199refinement
PHENIX1.14rc3_3199refinement
EM software
IDNameVersionCategory
4MotionCorr22_1.4.0CTF correction
10EMANinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63715 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Details: Model fitting into the cryo-EM map was performed using the programs UCSF Chimera (Pettersen et al., 2004), Namdinator (Kidmose et al., 2019), phenix.real_space_refine (Afonine et al., 2018) ...Details: Model fitting into the cryo-EM map was performed using the programs UCSF Chimera (Pettersen et al., 2004), Namdinator (Kidmose et al., 2019), phenix.real_space_refine (Afonine et al., 2018) and Coot (Emsley, Lohkamp, Scott, & Cowtan, 2010). Residues 500-1588 from the crystal structure of Se-Met mL-GDH180 (PDB code 7JSR) were fitted into the cryo-EM map. Se-methionine residues were replaced by methionine residues using Coot (Emsley et al., 2010) and the model was finally refined employing phenix.real_space_refine (Afonine et al., 2018) with NCS and secondary structure restraints.
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005833624
ELECTRON MICROSCOPYf_angle_d1.026245656
ELECTRON MICROSCOPYf_chiral_restr0.05975216
ELECTRON MICROSCOPYf_plane_restr0.00775996
ELECTRON MICROSCOPYf_dihedral_angle_d16.148820276

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