9DXU | pdb_00009dxu

Crystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

An mRNA-display derived cyclic peptide scaffold reveals the substrate binding interactions of an N-terminal cysteine oxidase.

Jiramongkol, Y.Patel, K.Johansen-Leete, J.Maxwell, J.W.C.Chang, Y.Du, J.J.Passioura, T.Cook, K.M.Payne, R.J.White, M.D.

(2025) Nat Commun 16: 4761-4761

  • DOI: https://doi.org/10.1038/s41467-025-59960-3
  • Primary Citation of Related Structures:  
    9DXB, 9DXU, 9DXV

  • PubMed Abstract: 

    N-terminal cysteine oxidases (NCOs) act as enzymatic oxygen (O 2 ) sensors, coordinating cellular changes to hypoxia in animals and plants. They regulate the O 2 -dependent stability of proteins bearing an N-terminal cysteine residue through the N-degron pathway. Despite their important role in hypoxic adaptation, which renders them potential therapeutic and agrichemical targets, structural information on NCO substrate binding remains elusive. To overcome this challenge, we employed a unique strategy by which a cyclic peptide inhibitor of the mammalian NCO, 2-aminoethanethiol dioxygenase (ADO), was identified by mRNA display and used as a scaffold to graft substrate moieties. This allowed the determination of two substrate analogue-bound crystal structures of ADO. Key binding interactions were revealed, including bidentate coordination of the N-terminal residue at the metal cofactor. Subsequent structure guided mutagenesis identified aspartate-206 as an essential catalytic residue, playing a role in reactive oxygen intermediate orientation or stabilisation. These findings provide fundamental information on ADO substrate interactions, which can elucidate enzyme mechanism and act as a platform for chemical discovery.


  • Organizational Affiliation
    • School of Chemistry, The University of Sydney, Sydney, NSW, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-aminoethanethiol dioxygenase271Homo sapiensMutation(s): 0 
Gene Names: ADOC10orf22
EC: 1.13.11.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SZ5 (Homo sapiens)
Explore Q96SZ5 
Go to UniProtKB:  Q96SZ5
PHAROS:  Q96SZ5
GTEx:  ENSG00000181915 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SZ5
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CP616synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
P [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth B]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.111α = 90
b = 71.605β = 90
c = 108.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia2008546

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release