8PMR | pdb_00008pmr

NADase from Aspergillus fumigatus with mutated calcium binding motif (D219A/E220A)

PDB DOI: https://doi.org/10.2210/pdb8PMR/pdb

Classification: HYDROLASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2023-06-29 Released: 2023-11-15
Deposition Author(s): Kallio, J.P., Ferrario, E., Stromland, O., Ziegler, M.
Funding Organization(s): Norwegian Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (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

Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase.

Ferrario, E., Kallio, J.P., Stromland, O., Ziegler, M.

(2023) Biochemistry 62: 3293-3302

PubMed: 37934975 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.3c00360
Primary Citation Related Structures:
8PMR, 8PMS

PubMed Abstract:
Nicotinamide adenine dinucleotide (NAD) is an essential molecule in all kingdoms of life, mediating energy metabolism and cellular signaling. Recently, a new class of highly active fungal surface NADases was discovered. The enzyme from the opportunistic human pathogen Aspergillus fumigatus was thoroughly characterized. It harbors a catalytic domain that resembles that of the tuberculosis necrotizing toxin from Mycobacterium tuberculosis , which efficiently cleaves NAD ⁺ to nicotinamide and ADP-ribose, thereby depleting the dinucleotide pool. Of note, the A. fumigatus NADase has an additional Ca ²⁺-binding motif at the C-terminus of the protein. Despite the presence of NADases in several fungal divisions, the Ca ²⁺-binding motif is uniquely found in the Eurotiales order, which contains species that have immense health and economic impacts on humans. To identify the potential roles of the metal ion-binding site in catalysis or protein stability, we generated and characterized A. fumigatus NADase variants lacking the ability to bind calcium. X-ray crystallographic analyses revealed that the mutation causes a drastic and dynamic structural rearrangement of the homodimer, resulting in decreased thermal stability. Even though the calcium-binding site is at a long distance from the catalytic center, the structural reorganization upon the loss of calcium binding allosterically alters the active site, thereby negatively affecting NAD-glycohydrolase activity. Together, these findings reveal that this unique calcium-binding site affects the protein fold, stabilizing the dimeric structure, but also mediates long-range effects resulting in an increased catalytic rate.

Organizational Affiliation

Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway.

Macromolecule Content

Total Structure Weight: 116.4 kDa
Atom Count: 7,617
Modeled Residue Count: 836
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA	A, B, C, D	248	Aspergillus fumigatus Af293	Mutation(s): 2 Gene Names: nadA, AFUA_6G14470 EC: 3.2.2.5 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt
Find proteins for Q4WL81 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WL81 Go to UniProtKB: Q4WL81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WL81
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I	2		N-Glycosylation	Interactions Focus chain G Focus chain I Interactions & Density Focus chain G Focus chain I
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	5		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 6
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	J, K, L	3		N-Glycosylation	Interactions Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	N [auth B], P [auth C], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B]	M [auth A], O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Interactions & Density Focus chain M [auth A] Focus chain O [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth D]	Q [auth C], R [auth C], U [auth D], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain W [auth D] Interactions & Density Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]