9GTJ | pdb_00009gtj

Chlorite dismutase from Pseudomonas sp.

PDB DOI: https://doi.org/10.2210/pdb9GTJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-18 Released: 2025-06-11
Deposition Author(s): Papageorgiou, A.C., Chronopoulou, E.G.
Funding Organization(s): iNEXT-Discovery

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free:
0.161 (Depositor), 0.158 (DCC)
R-Value Work:
0.143 (Depositor), 0.142 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Biochemical and structural characterization of chlorite dismutase enzyme from Pseudomonas aeruginosa.

Nokas, D.V., Panagiotopoulou, E.K., Kapogiannatos, A.I., Premetis, G.E., Labrou, N.E., Efthimiadou, E.K., Papageorgiou, A.C., Chronopoulou, E.G.

(2025) FEBS J

PubMed: 40458033 Search on PubMed
DOI: https://doi.org/10.1111/febs.70151
Primary Citation of Related Structures:
9GTJ

PubMed Abstract:
Industrialization and urbanization have caused serious contamination of water bodies, and the removal of chemical contaminants has become a major challenge. Chlorite is a harmful anthropogenic compound with a serious environmental impact and has been detected in groundwater, drinking water, and soil. Enzymes are considered sustainable tools for bioremediation, with chlorite dismutase (Cld) being a notable example. This enzyme has unique properties owing to the rare dioxygen bond formation that it catalyzes. In the present study, we report the cloning, biochemical, and structural characterization of the dimeric Cld from Pseudomonas aeruginosa (PaCld). PaCld is a heme b oxidoreductase that can decompose chlorite ( $ClO$ 2 - $$ {\mathrm{ClO}}_2^{-} $$ or OClO ^-) into harmless chloride (Cl ^-) and dioxygen (O ₂) with high turnover rates. The structure of PaCld was determined at atomic (0.99 Å) resolution using X-ray crystallography. Additionally, steady-state kinetics and stability studies provided valuable insights into the catalytic mechanism of dimeric Clds. Apart from chlorite bioremediation of water, Clds can also be used in biomedical and synthetic biology as well as in enzymatic cascades with O ₂-utilizing enzymes.

Organizational Affiliation

Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Greece.

Macromolecule Content

Total Structure Weight: 45.77 kDa
Atom Count: 3,867
Modeled Residue Count: 370
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorite dismutase	A, B	193	Pseudomonas	Mutation(s): 0 Gene Names: SAMN05216605_1413
UniProt
Find proteins for A4VPS8 (Stutzerimonas stutzeri (strain A1501)) Explore A4VPS8 Go to UniProtKB: A4VPS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4VPS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]