7F77 | pdb_00007f77

Crystal structure of glutamate dehydrogenase 3 from Candida albicans

• PDB DOI: https://doi.org/10.2210/pdb7F77/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli BL21(DE3)
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free: 
  0.290 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

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 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.
Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China.
Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China. Electronic address: [e-mail].
Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 158.62 kDa 
• Atom Count: 9,733 
• Modeled Residue Count: 1,269 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free:  0.290 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.542	α = 90
b = 94.542	β = 90
c = 334.32	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 

Deposition Data

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

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