Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content

• Total Structure Weight: 142.81 kDa 
• Atom Count: 10987 
• Modelled Residue Count: 1190 
• Deposited Residue Count: 1205 
• Unique protein chains: 1

3NN1

Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with imidazole

• DOI: 10.2210/pdb3NN1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitrospira defluvii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-23 Released: 2010-07-28 
• Deposition Author(s): Kostan, J., Sjoeblom, B., Maixner, F., Mlynek, G., Furtmueller, P.G., Obinger, C., Wagner, M., Daims, H., Djinovic-Carugo, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue

Kostan, J., Sjoeblom, B., Maixner, F., Mlynek, G., Furtmueller, P.G., Obinger, C., Wagner, M., Daims, H., Djinovic-Carugo, K.

(2010) J Struct Biol 172: 331-342

• PubMed: 20600954 
• DOI: 10.1016/j.jsb.2010.06.014
• Primary Citation of Related Structures:  
  3NN1, 3NN2, 3NN3, 3NN4


• PubMed Abstract: 
  

Chlorite dismutase (Cld) is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen (reaction: ClO(2)(-)→Cl(-)+O(2)). Since bacteria with Cld play significant roles in the bioremediation of industrially contaminated sites and also in wastewater treatment, it is of high interest to understand the molecular mechanism of chlorite detoxification. Here we investigate a highly active Cld from Candidatus Nitrospira defluvii (NdCld), a key nitrifier in biological wastewater treatment, using a comprehensive structural, biochemical and bioinformatics approach. We determined the crystal structure of Cld from Candidatus Nitrospira defluvii and showed that functional NdCld is a homopentamer possessing a fold found in other Clds and Cld-like enzymes. To investigate the Cld function in more detail, site-directed mutagenesis of a catalytically important residue (Arg173) was performed and two enzyme mutants were structurally and biochemically characterized. Arginine 173 is demonstrated to play a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction. The flexible residue modulates the electrostatic potential and size of the active site entrance and might be involved in keeping transiently formed hypochlorite in place for final molecular oxygen and chloride formation. Furthermore, using a structure-based sequence alignment, we show that the residue corresponding to Arg173 is conserved in all known active forms of Cld and propose it as a marker for Cld activity in yet uncharacterized Cld-like proteins. Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor.

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Organizational Affiliation: 

Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorite dismutase	A, B, C, D, E	241	Nitrospira defluvii	Mutation(s): 0  Gene Names: cld, cld1, NIDE1387 EC: 1.13.11.49
Find proteins for B3U4H7 (Nitrospira defluvii) Explore B3U4H7  Go to UniProtKB:  B3U4H7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B, C, D, E	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	A, B, C, D, E	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IMD	A, B, C, D, E	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	A, B, C, D, E	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.67	α = 90
b = 145.67	β = 90
c = 136.44	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-23 
• Released Date: 2010-07-28 
Deposition Author(s): Kostan, J., Sjoeblom, B., Maixner, F., Mlynek, G., Furtmueller, P.G., Obinger, C., Wagner, M., Daims, H., Djinovic-Carugo, K.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance