7F79

Crystal structure of glutamate dehydrogenase 3 from Candida albicans in complex with alpha-ketoglutarate and NADPH

• PDB DOI: https://doi.org/10.2210/pdb7F79/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-28 Released: 2021-07-21 
• Deposition Author(s): Li, N., Wang, W., Zeng, X., Liu, M., Li, M., Li, C., Wang, M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal structure of glutamate dehydrogenase 3 from Candida albicans.

Li, N., Wang, W., Zeng, X., Liu, M., Li, M., Li, C., Wang, M.

(2021) Biochem Biophys Res Commun 570: 15-20

• PubMed: 34271431 
• DOI: https://doi.org/10.1016/j.bbrc.2021.07.014
• Primary Citation of Related Structures:  
  7F77, 7F79


• PubMed Abstract: 
  

  Glutamate dehydrogenase 3 from Candida albicans (CaGdh3) catalyzes the reversible oxidative deamination of l-glutamate, playing an important role in the yeast-to-hyphal transition of C. albicans. Here we report the crystal structures of CaGdh3 and its complex with α-ketoglutarate and NADPH. CaGdh3 exists as a hexamer, with each subunit containing two domains. The substrate and coenzyme bind in the cleft between the two domains and their binding induces a conformational change in CaGdh3. Our results will help to understand the catalytic mechanism of CaGdh3 and will provide a structural basis for the design of antifungal drugs targeting the CaGdh3 pathway.

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Organizational Affiliation: 

Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 323.04 kDa 
• Atom Count: 21,545 
• Modelled Residue Count: 2,723 
• Deposited Residue Count: 2,904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E, F	484	Candida albicans SC5314	Mutation(s): 0  Gene Names: GDH3
UniProt
Find proteins for A0A1D8PMH8 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore A0A1D8PMH8  Go to UniProtKB:  A0A1D8PMH8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	G [auth A], J [auth B], M [auth C], O [auth D], S [auth E], V [auth F]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
AKG (Subject of Investigation/LOI)	H [auth A], K [auth B], N [auth C], P [auth D], T [auth E], W [auth F]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	I [auth A], L [auth B], Q [auth D], R [auth D], U [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.279	α = 90
b = 155.224	β = 95.5
c = 98.807	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Li, N., Wang, W., Zeng, X., Liu, M., Li, M., Li, C., Wang, M.

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Funding Organization	Location	Grant Number
Other government	China	1808085MC53

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description