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Title: The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1

Abstract

The ring-hydroxylating dioxygenase (RHD) from Sphingomonas CHY-1 is remarkable due to its ability to initiate the oxidation of a wide range of polycyclic aromatic hydrocarbons (PAHs), including PAHs containing four- and five-fused rings, known pollutants for their toxic nature. Although the terminal oxygenase from CHY-1 exhibits limited sequence similarity with well characterized RHDs from the naphthalene dioxygenase family, the crystal structure determined to 1.85 {angstrom} by molecular replacement revealed the enzyme to share the same global {alpha}{sub 3}{beta}{sub 3} structural pattern. The catalytic domain distinguishes itself from other bacterial non-heme Rieske iron oxygenases by a substantially larger hydrophobic substrate binding pocket, the largest ever reported for this type of enzyme. While residues in the proximal region close to the mononuclear iron atom are conserved, the central region of the catalytic pocket is shaped mainly by the side chains of three amino acids, Phe350, Phe404 and Leu356, which contribute to the rather uniform trapezoidal shape of the pocket. Two flexible loops, LI and LII, exposed to the solvent seem to control the substrate access to the catalytic pocket and control the pocket length. Compared with other naphthalene dioxygenases residues Leu223 and Leu226, on loop LI, are moved towards the solvent, thusmore » elongating the catalytic pocket by at least 2 {angstrom}. An 11 {angstrom} long water channel extends from the interface between the {alpha} and {beta} subunits to the catalytic site. The comparison of these structures with other known oxygenases suggests that the broad substrate specificity presented by the CHY-1 oxygenase is primarily due to the large size and particular topology of its catalytic pocket and provided the basis for the study of its reaction mechanism.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
929798
Report Number(s):
BNL-80345-2008-JA
TRN: US200822%%1017
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: FEBS Journal; Journal Volume: 274
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; AMINO ACIDS; ATOMS; CRYSTAL STRUCTURE; ENZYMES; INTERFACES; IRON; NAPHTHALENE; OXIDATION; OXYGENASES; POLLUTANTS; POLYCYCLIC AROMATIC HYDROCARBONS; REACTION KINETICS; RESIDUES; SOLVENTS; SPECIFICITY; SUBSTRATES; TOPOLOGY; national synchrotron light source

Citation Formats

Jakoncic,J., Jouanneau, Y., Meyer, C., and Stojanoff, V.. The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1. United States: N. p., 2007. Web. doi:10.1111/j.1742-4658.2007.05783.x.
Jakoncic,J., Jouanneau, Y., Meyer, C., & Stojanoff, V.. The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1. United States. doi:10.1111/j.1742-4658.2007.05783.x.
Jakoncic,J., Jouanneau, Y., Meyer, C., and Stojanoff, V.. Mon . "The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1". United States. doi:10.1111/j.1742-4658.2007.05783.x.
@article{osti_929798,
title = {The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1},
author = {Jakoncic,J. and Jouanneau, Y. and Meyer, C. and Stojanoff, V.},
abstractNote = {The ring-hydroxylating dioxygenase (RHD) from Sphingomonas CHY-1 is remarkable due to its ability to initiate the oxidation of a wide range of polycyclic aromatic hydrocarbons (PAHs), including PAHs containing four- and five-fused rings, known pollutants for their toxic nature. Although the terminal oxygenase from CHY-1 exhibits limited sequence similarity with well characterized RHDs from the naphthalene dioxygenase family, the crystal structure determined to 1.85 {angstrom} by molecular replacement revealed the enzyme to share the same global {alpha}{sub 3}{beta}{sub 3} structural pattern. The catalytic domain distinguishes itself from other bacterial non-heme Rieske iron oxygenases by a substantially larger hydrophobic substrate binding pocket, the largest ever reported for this type of enzyme. While residues in the proximal region close to the mononuclear iron atom are conserved, the central region of the catalytic pocket is shaped mainly by the side chains of three amino acids, Phe350, Phe404 and Leu356, which contribute to the rather uniform trapezoidal shape of the pocket. Two flexible loops, LI and LII, exposed to the solvent seem to control the substrate access to the catalytic pocket and control the pocket length. Compared with other naphthalene dioxygenases residues Leu223 and Leu226, on loop LI, are moved towards the solvent, thus elongating the catalytic pocket by at least 2 {angstrom}. An 11 {angstrom} long water channel extends from the interface between the {alpha} and {beta} subunits to the catalytic site. The comparison of these structures with other known oxygenases suggests that the broad substrate specificity presented by the CHY-1 oxygenase is primarily due to the large size and particular topology of its catalytic pocket and provided the basis for the study of its reaction mechanism.},
doi = {10.1111/j.1742-4658.2007.05783.x},
journal = {FEBS Journal},
number = ,
volume = 274,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}