4RWM

Kuenenia stuttgartiensis hydroxylamine oxidoreductase cryoprotected with ethylene glycol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

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This is version 2.1 of the entry. See complete history. 


Literature

An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase.

Dietl, A., Maalcke, W., Barends, T.R.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1708-1713

  • DOI: https://doi.org/10.1107/S1399004715010706
  • Primary Citation of Related Structures:  
    4RWM

  • PubMed Abstract: 

    Hydroxylamine oxidoreductases (HAOs) contain a unique haem cofactor called P460 that consists of a profoundly ruffled c-type haem with two covalent bonds between the haem porphyrin and a conserved tyrosine. This cofactor is exceptional in that it abstracts electrons from a ligand bound to the haem iron, whereas other haems involved in redox chemistry usually inject electrons into their ligands. The effects of the tyrosine cross-links and of the haem ruffling on the chemistry of this cofactor have been investigated theoretically but are not yet clear. A new crystal structure of an HAO from Candidatus Kuenenia stuttgartiensis, a model organism for anaerobic ammonium oxidation, now shows that its P460 cofactor has yet another unexpected reactivity: when ethylene glycol was used as a cryoprotectant, the 1.8 Å resolution electron-density maps showed additional density which could be interpreted as an ethylene glycol molecule covalently bound to the C16 atom of the haem ring, opposite the covalent links to the conserved tyrosine. Possible causes for this unexpected reactivity are discussed.

    • Organizational Affiliation: 

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Similar to hydroxylamine oxidoreductase hao500Candidatus Kuenenia stuttgartiensisMutation(s): 0 
EC: 1.7.3.4 (PDB Primary Data), 1.7.2.9 (UniProt)
UniProt
Find proteins for Q1PX48 (Kuenenia stuttgartiensis)
Explore Q1PX48 
Go to UniProtKB:  Q1PX48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1PX48
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC
Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HG1
Query on HG1
Download Ideal Coordinates CCD File 
J [auth A]1-[(4-cyclohexylbutanoyl)(2-hydroxyethyl)amino]-1-deoxy-D-glucitol
C18 H35 N O7
XAMJEPWYNXYYBT-BURFUSLBSA-N
PO4
Query on PO4
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.29α = 90
b = 130.29β = 90
c = 130.29γ = 90
Software Package:
Software NamePurpose
HEIDIdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 2.0: 2021-03-10
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary