1NDO

NAPHTHALENE 1,2-DIOXYGENASE

• PDB DOI:  https://doi.org/10.2210/pdb1NDO/pdb

• Classification: NON-HEME IRON DIOXYGENASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-01-11 Released: 1999-03-23 
• Deposition Author(s): Ramaswamy, S., Kauppi, B., Carredano, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.190 
• R-Value Observed: 0.220 

Literature

Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.

Kauppi, B., Lee, K., Carredano, E., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

(1998) Structure 6: 571-586

• PubMed: 9634695 
• DOI: https://doi.org/10.1016/s0969-2126(98)00059-8
• Primary Citation of Related Structures:  
  1NDO


• PubMed Abstract: 
  

Pseudomonas sp. NCIB 9816-4 utilizes a multicomponent enzyme system to oxidize naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. The enzyme component catalyzing this reaction, naphthalene 1,2-dioxygenase (NDO), belongs to a family of aromatic-ring-hydroxylating dioxygenases that oxidize aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilize a mononuclear non-heme iron center to catalyze the addition of dioxygen to their respective substrates. The present study was conducted to provide essential structural information necessary for elucidating the mechanism of action of NDO.

---

Organizational Affiliation: 

Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 218.6 kDa 
• Atom Count: 16,326 
• Modelled Residue Count: 1,918 
• Deposited Residue Count: 1,929 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAPHTHALENE 1,2-DIOXYGENASE	A, C, E	449	Pseudomonas putida	Mutation(s): 0  Gene Names: NAHACAD, ndoB, nahA3, nahAC, ndoC2 EC: 1.14.12.12
UniProt
Find proteins for P0A110 (Pseudomonas putida) Explore P0A110  Go to UniProtKB:  P0A110

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAPHTHALENE 1,2-DIOXYGENASE	B, D, F	194	Pseudomonas putida	Mutation(s): 0  Gene Names: NAHACAD, ndoC, nahAD EC: 1.14.12.12
UniProt
Find proteins for P0A112 (Pseudomonas putida) Explore P0A112  Go to UniProtKB:  P0A112

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	H [auth A], J [auth C], L [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE	G [auth A], I [auth C], K [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.190 
• R-Value Observed: 0.220 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105	α = 90
b = 174	β = 90
c = 282.5	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Ramaswamy, S., Kauppi, B., Carredano, E.

Revision History  

• Version 1.0: 1999-03-23
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance