8XCO

Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH in the initial stage of reaction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.

Wakabayashi, T.Oide, M.Nakasako, M.

(2024) Sci Rep 14: 11165-11165

  • DOI: https://doi.org/10.1038/s41598-024-61793-x
  • Primary Citation of Related Structures:  
    8XCO, 8XCP, 8XCQ, 8XCR, 8XCS, 8XCT, 8XCU, 8XCV, 8XCW, 8XCX, 8XCY, 8XCZ, 8XD0, 8XD1, 8XD2, 8XD3, 8XD4, 8XD5, 8XD6

  • PubMed Abstract: 

    Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis-Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.


  • Organizational Affiliation

    Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase419Thermococcus profundusMutation(s): 0 
Gene Names: gdhA
EC: 1.4.1.3
UniProt
Find proteins for O74024 (Thermococcus profundus)
Explore O74024 
Go to UniProtKB:  O74024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74024
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japanjp13480214
Japan Society for the Promotion of Science (JSPS)Japanjp19204042
Japan Society for the Promotion of Science (JSPS)Japanjp22244054
Japan Society for the Promotion of Science (JSPS)Japanjp21H01050
Japan Society for the Promotion of Science (JSPS)Japanjp26800227
Japan Society for the Promotion of Science (JSPS)Japanjp18J11653
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp15076210
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp20050030
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp22018027
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp23120525
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp25120725
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp15H01647
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp17H05891
Japan Science and TechnologyJapanJPMJPR22E2

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references