6YGG | pdb_00006ygg

NADase from Aspergillus fumigatus complexed with a substrate anologue

• PDB DOI: https://doi.org/10.2210/pdb6YGG/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus fumigatus Af293
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-03-27 Released: 2020-12-23 
• Deposition Author(s): Stromland, O., Ziegler, M., Kallio, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.226 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Discovery of fungal surface NADases predominantly present in pathogenic species.

Stromland, O., Kallio, J.P., Pschibul, A., Skoge, R.H., Hardardottir, H.M., Sverkeli, L.J., Heinekamp, T., Kniemeyer, O., Migaud, M., Makarov, M.V., Gossmann, T.I., Brakhage, A.A., Ziegler, M.

(2021) Nat Commun 12: 1631-1631

• PubMed: 33712585 
• DOI: https://doi.org/10.1038/s41467-021-21307-z
• Primary Citation Related Structures: 
  6YGE, 6YGF, 6YGG


• PubMed Abstract: 
  

  Nicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host's NAD ⁺ pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca ²⁺ -binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.

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Organizational Affiliation: 
• Department of Biomedicine, University of Bergen, Bergen, Norway.
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.
Department of Biological Sciences, University of Bergen, Bergen, Norway.
Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.
Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
Department of Biomedicine, University of Bergen, Bergen, Norway. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 59 kDa 
• Atom Count: 3,998 
• Modeled Residue Count: 418 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AfNADase	A, B	248	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: AFUA_6G14470 EC: 3.2.2 (UniProt), 3.2.2.5 (UniProt)
UniProt
Find proteins for Q4WL81 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WL81  Go to UniProtKB:  Q4WL81
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, E, F, G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQV (Subject of Investigation/LOI)	K [auth B]	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) C22 H28 N6 O14 P2 HNKKJJHKTPALEK-RACQCECLSA-N
NAG	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)	I [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.226 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.05	α = 90
b = 64.318	β = 90
c = 161.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
Aimless	data scaling
PHASER	phasing
Coot	model building
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Stromland, O., Ziegler, M., Kallio, J.P.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary