8C0Z

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


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 1.1 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

  • DOI: https://doi.org/10.1126/sciadv.adg6689
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde:ferredoxin oxidoreductase,tungsten-containing
A, B
616Aromatoleum aromaticumMutation(s): 0 
Gene Names: ebA5005
EC: 1.2.7
UniProt
Find proteins for Q5P143 (Aromatoleum aromaticum (strain EbN1))
Explore Q5P143 
Go to UniProtKB:  Q5P143
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5P143
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur cluster-binding protein potential subunit of aldehyde oxidoreductaseC,
E [auth F]
192Aromatoleum aromaticumMutation(s): 0 
Gene Names: ebA5004
UniProt
Find proteins for Q5P144 (Aromatoleum aromaticum (strain EbN1))
Explore Q5P144 
Go to UniProtKB:  Q5P144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5P144
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Similar to ferredoxin:NADH oxidoreductases or NADH oxidases,potential subunit of aldehyde oxidoreductaseD [auth E]424Aromatoleum aromaticumMutation(s): 0 
Gene Names: TM0395ebA5007
UniProt
Find proteins for Q5P142 (Aromatoleum aromaticum (strain EbN1))
Explore Q5P142 
Go to UniProtKB:  Q5P142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5P142
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T7R (Subject of Investigation/LOI)
Query on T7R

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
tungsten cofactor
C20 H24 N10 O14 P2 S4 W
KOSOUPJZBKQLDF-RRYOYCSRSA-J
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
R [auth E]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
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
BEZ
Query on BEZ

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • 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 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union--
Polish National Science CentrePoland--
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references