9T62 | pdb_00009t62

Crystal structure of ortho-aminophenol oxidase SmNspF from Streptomyces murayamaensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.238 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.183 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into ortho -aminophenol oxidases: kinetic and crystallographic characterization of Sm NspF and Sg GriF.

Le Xuan, H.Rompel, A.

(2026) Inorg Chem Front 13: 3786-3794

  • DOI: https://doi.org/10.1039/d5qi02495a
  • Primary Citation Related Structures: 
    9T62

  • PubMed Abstract: 

    Actinobacteria-derived o -aminophenol oxidases (AOs) represent a largely unexplored subclass of type-III copper enzymes with catalytic properties distinct from tyrosinases and catechol oxidases. The determination of the first crystal structure of an AO ( Sm NspF) displays unique loop insertions and important second-sphere amino acids in vicinity of the binuclear copper center. The substrate-guiding effect of the second activity controller (His B2+1 ) influences the binding affinity for carboxyl-containing substrates in the AOs Sm NspF and Sg GriF. Thus, kinetic investigations reveal both overlapping and distinct substrate preferences for Sm NspF and Sg GriF: while both enzymes oxidize monophenols, o -aminophenols, and o -diphenols, they do so at significantly different reaction rates. Sm NspF preferentially oxidizes carboxylated substrates such as 3,4-dihydroxybenzoic acid and 3-amino-4-hydroxybenzoic acid, whereas Sg GriF exhibits higher activity toward para -methylated analogs, including 4-methylcatechol and 2-amino-4-methylphenol. Remarkably, both enzymes display enzymatic activities beyond the known AO reactivity spectrum by oxidizing 2-aminoresorcinol and o -phenylenediamine, which underlies the high versatility of the binuclear copper center. Altogether, these findings provide a structural basis for AO's enzymatic activity and broaden the known catalytic spectrum, which enables the prediction of catalytic properties in type-III copper proteins based on their amino acid sequence.


  • Organizational Affiliation
    • Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie Josef-Holaubek Platz 2 1090 Vienna Austria annette.rompel@univie.ac.at https://www.bpc.univie.ac.at.

Macromolecule Content 

  • Total Structure Weight: 72.1 kDa 
  • Atom Count: 5,010 
  • Modeled Residue Count: 599 
  • Deposited Residue Count: 614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-aminophenol oxidase
A, B
307Streptomyces murayamaensisMutation(s): 0 
Gene Names: nspF
UniProt
Find proteins for D6RTB9 (Streptomyces murayamaensis)
Explore D6RTB9 
Go to UniProtKB:  D6RTB9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6RTB9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.238 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.183 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.189α = 90
b = 86.189β = 90
c = 88.245γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
gemmidata extraction
autoPROCdata reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentAustria10.55776/P32932

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Database references
  • Version 1.2: 2026-05-13
    Changes: Database references