4N4J

Kuenenia stuttgartiensis hydroxylamine oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases.

Maalcke, W.J.Dietl, A.Marritt, S.J.Butt, J.N.Jetten, M.S.Keltjens, J.T.Barends, T.R.Kartal, B.

(2014) J Biol Chem 289: 1228-1242

  • DOI: 10.1074/jbc.M113.525147
  • Primary Citation of Related Structures:  
    4N4J, 4N4K, 4N4L, 4N4M, 4N4N, 4N4O

  • PubMed Abstract: 
  • Nitric oxide is an important molecule in all domains of life with significant biological functions in both pro- and eukaryotes. Anaerobic ammonium-oxidizing (anammox) bacteria that contribute substantially to the release of fixed nitrogen into the atmosphere use the oxidizing power of NO to activate inert ammonium into hydrazine (N2H4) ...

    Nitric oxide is an important molecule in all domains of life with significant biological functions in both pro- and eukaryotes. Anaerobic ammonium-oxidizing (anammox) bacteria that contribute substantially to the release of fixed nitrogen into the atmosphere use the oxidizing power of NO to activate inert ammonium into hydrazine (N2H4). Here, we describe an enzyme from the anammox bacterium Kuenenia stuttgartiensis that uses a novel pathway to make NO from hydroxylamine. This new enzyme is related to octaheme hydroxylamine oxidoreductase, a key protein in aerobic ammonium-oxidizing bacteria. By a multiphasic approach including the determination of the crystal structure of the K. stuttgartiensis enzyme at 1.8 Å resolution and refinement and reassessment of the hydroxylamine oxidoreductase structure from Nitrosomonas europaea, both in the presence and absence of their substrates, we propose a model for NO formation by the K. stuttgartiensis enzyme. Our results expand the understanding of the functions that the widespread family of octaheme proteins have.


    Organizational Affiliation

    From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525AJ Nijmegen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hydroxylamine oxidoreductaseA500Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: haohao_3hoxKsCSTR_43280KSMBR1_2670kustc1061
EC: 1.7.3.4 (PDB Primary Data), 1.7.2.8 (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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HG1
Query on HG1

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1-[(4-cyclohexylbutanoyl)(2-hydroxyethyl)amino]-1-deoxy-D-glucitol
C18 H35 N O7
XAMJEPWYNXYYBT-BURFUSLBSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130α = 90
b = 130β = 90
c = 130γ = 90
Software Package:
Software NamePurpose
HEIDIdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 2.0: 2020-03-18
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary