Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 74194.41 
• Atom Count: 5179 
• Residue Count: 643 
• Unique protein chains: 2

2HMJ

Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.

• DOI: 10.2210/pdb2HMJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas sp. (strain C18)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2006-07-11 Released: 2006-10-10 
• Deposition Author(s): Ferraro, D.J., Okerlund, A.L., Mowers, J.C., Ramaswamy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 

Literature

Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase.

Ferraro, D.J., Okerlund, A.L., Mowers, J.C., Ramaswamy, S.

(2006) J.Bacteriol. 188: 6986-6994

• PubMed: 16980501 
• DOI: 10.1128/JB.00707-06
• Primary Citation of Related Structures:  
  2HMO, 2HMN, 2HMM, 2HML, 2HMK


• PubMed Abstract: 
  

Rieske oxygenase (RO) systems are two- and three-component enzyme systems that catalyze the formation of cis-dihydrodiols from aromatic substrates. Degradation of pollutants in contaminated soil and generation of chiral synthons have been the major foci of RO research. Substrate specificity and product regio- and stereoselectivity have been shown to vary between individual ROs. While directed evolution methods for altering RO function have been successful in the past, rational engineering of these enzymes still poses a challenge due to the lack of structural understanding. Here we examine the structural changes induced by mutation of Phe-352 in naphthalene 1,2-dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NDO-O(9816-4)). Structures of the Phe-352-Val mutant in native form and in complex with phenanthrene and anthracene, along with those of wild-type NDO-O(9816-4) in complex with phenanthrene, anthracene, and 3-nitrotoluene, are presented. Phenanthrene was shown to bind in a different orientation in the Phe-352-Val mutant active site from that in the wild type, while anthracene was found to bind in similar positions in both enzymes. Two orientations of 3-nitrotoluene were observed, i.e., a productive and a nonproductive orientation. These orientations help explain why NDO-O(9816-4) forms different products from 3-nitrotoluene than those made from nitrobenzene dioxygenase. Comparison of these structures among themselves and with other known ROs bound to substrates reveals that the orientation of substrate binding at the active site is the primary determinant of product regio- and stereoselectivity.

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Organizational Affiliation: 

Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 BSB, Iowa City, IA 52242, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Naphthalene 1,2-dioxygenase alpha subunit	A	449	Pseudomonas sp. (strain C18)	Mutations: V352F Gene Names: doxB EC: 1.14.12.12
Find proteins for P0A111 (Pseudomonas sp. (strain C18)) Go to UniProtKB:  P0A111

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Naphthalene 1,2-dioxygenase beta subunit	B	194	Pseudomonas sp. (strain C18)	Gene Names: doxD
Find proteins for P0A113 (Pseudomonas sp. (strain C18)) Go to UniProtKB:  P0A113

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	A, B	ethane-1,2-diol ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FES	A	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE	A	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 139.894	α = 90.00
b = 139.894	β = 90.00
c = 208.580	γ = 120.00

Software Package:

Software Name	Purpose
d*TREK	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-11 
• Released Date: 2006-10-10 
• Deposition Author(s): Ferraro, D.J., Okerlund, A.L., Mowers, J.C., Ramaswamy, S.

Revision History 

• Version 1.0: 2006-10-10
  Type: Initial release
• Version 1.1: 2007-10-16
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2012-09-12
  Type: Other