Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation, gel filtration

Macromolecule Content

• Total Structure Weight: 63.38 kDa 
• Atom Count: 4872 
• Modelled Residue Count: 497 
• Deposited Residue Count: 500 
• Unique protein chains: 1

4N4J

Kuenenia stuttgartiensis hydroxylamine oxidoreductase

• PDB DOI: 10.2210/pdb4N4J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Candidatus Kuenenia stuttgartiensis
• Mutation(s): No 


• Deposited: 2013-10-08 Released: 2013-12-11 
• Deposition Author(s): Maalcke, W.J., Dietl, A., Marritt, S.J., Butt, J.N., Jetten, M.S.M., Keltjens, J.T., Barends, T.R.M.B., Kartal, B.

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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 

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

• PubMed: 24302732 
• 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). 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydroxylamine oxidoreductase	A	500	Candidatus Kuenenia stuttgartiensis	Mutation(s): 0  Gene Names: hao, hao_3, hox, KsCSTR_43280, KSMBR1_2670, kustc1061 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	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
HG1	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
PO4	B [auth A], C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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 = 130	α = 90
b = 130	β = 90
c = 130	γ = 90

Software Package:

Software Name	Purpose
HEIDI	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-08 
• Released Date: 2013-12-11 
Deposition Author(s): Maalcke, W.J., Dietl, A., Marritt, S.J., Butt, J.N., Jetten, M.S.M., Keltjens, J.T., Barends, T.R.M.B., Kartal, B.

Revision History  

• 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