8C0Z | pdb_00008c0z

CryoEM structure of a tungsten-containing aldehyde oxidoreductase from Aromatoleum aromaticum

PDB DOI: https://doi.org/10.2210/pdb8C0Z/pdb
EM Map EMD-16376: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Aromatoleum aromaticum
Expression System: Aromatoleum evansii
Mutation(s): No

Deposited: 2022-12-19 Released: 2023-05-31
Deposition Author(s): Winiarska, A., Ramirez-Amador, F., Hege, D., Gemmecker, Y., Prinz, S., Hochberg, G., Heider, J., Szaleniec, M., Schuller, J.M.
Funding Organization(s): European Union (EU), Polish National Science Centre, German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Resolution: 3.22 Å
Resolution: 3.22 Å
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire.

Winiarska, A., Ramirez-Amador, F., Hege, D., Gemmecker, Y., Prinz, S., Hochberg, G., Heider, J., Szaleniec, M., Schuller, J.M.

(2023) Sci Adv 9: eadg6689-eadg6689

PubMed: 37267359 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adg6689
Primary Citation Related Structures:
8C0Z

PubMed Abstract:
Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacterium Aromatoleum aromaticum (AOR _Aa) consists of three different subunits (AorABC) and uses nicotinamide adenine dinucleotide (NAD) as an electron acceptor. Here, we reveal that the enzyme forms filaments of repeating AorAB protomers that are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with quantum mechanics:molecular mechanics (QM:MM)-based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology.

Organizational Affiliation

Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland.

Macromolecule Content

Total Structure Weight: 225.36 kDa
Atom Count: 15,083
Modeled Residue Count: 1,972
Deposited Residue Count: 2,040
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde:ferredoxin oxidoreductase,tungsten-containing	A, B	616	Aromatoleum aromaticum	Mutation(s): 0 Gene Names: ebA5005 EC: 1.2.7
UniProt
Find proteins for Q5P143 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1)) Explore Q5P143 Go to UniProtKB: Q5P143
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5P143
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster-binding protein potential subunit of aldehyde oxidoreductase	C, E [auth F]	192	Aromatoleum aromaticum	Mutation(s): 0 Gene Names: ebA5004
UniProt
Find proteins for Q5P144 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1)) Explore Q5P144 Go to UniProtKB: Q5P144
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5P144
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Similar to ferredoxin:NADH oxidoreductases or NADH oxidases,potential subunit of aldehyde oxidoreductase	D [auth E]	424	Aromatoleum aromaticum	Mutation(s): 0 Gene Names: TM0395, ebA5007
UniProt
Find proteins for Q5P142 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1)) Explore Q5P142 Go to UniProtKB: Q5P142
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5P142
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T7R (Subject of Investigation/LOI) Query on T7R Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	tungsten cofactor C₂₀ H₂₄ N₁₀ O₁₄ P₂ S₄ W KOSOUPJZBKQLDF-RRYOYCSRSA-J		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E] mmCIF format, chain R [auth E]	R [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain R [auth E] Interactions & Density Focus chain R [auth E]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain V [auth F] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F]	F [auth A] M [auth B] N [auth C] O [auth C] P [auth C] F [auth A], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], S [auth F], T [auth F], U [auth F], V [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth F]
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]