7F79 | pdb_00007f79

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1D8PMH8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] J [auth B] M [auth C] O [auth D] S [auth E] 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		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain S [auth E] Focus chain V [auth F]
AKG (Subject of Investigation/LOI) Query on AKG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	H [auth A] K [auth B] N [auth C] P [auth D] T [auth E] 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		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain W [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain U [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E]	I [auth A], L [auth B], Q [auth D], R [auth D], U [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	1808085MC53

Revision History (Full details and data files)

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

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

Crystal structure of glutamate dehydrogenase 3 from Candida albicans.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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