| Root |
Created: 13 July 1998
| Iron centre | Iron ligands | Formal iron oxidation/spin states |
||
|---|---|---|---|---|
| I |   Cys)2(N His)2 |
[Fe2S2]2+ (S=0) |
||
| Cys
|
His
|
|||
| II |   His)2OAsp·H2O |
His;
H2O |
||
Bacterial aromaticringhydroxylating dioxygenases incorporate two
atoms of dioxygen (O2) into their substrates in the dixydroxylation
reaction (1). The product is (substituted)
cis1,2dihydroxycyclohexadiene, which is
subsequently converted to (substituted) benzene glycol by a
cisdiol dehydrogenase (2)
[1]:
The 3D structure of the hydroxylase component of naphthalene
1,2dioxygenase from Pseudomonas has been determined
[4].
The protein is an (
A large family of multicomponent mononuclear (nonhaem) iron oxygenases
has been identified
[2,
3].
Components of bacterial aromaticring dioxygenases constitute two
different functional classes: hydroxylase components and electron transfer
components. Hydroxylase components are either
(
(1)
(2)
ß)n or
()n oligomers.
Two prosthetic groups, a Riesketype [Fe2S2] centre
and a mononuclear iron, are associated with the
subunit in the
(ß)ntype
enzymes.
Electron transfer components are composed of flavoprotein
(NADH:ferredoxin oxidoreductase) and Riesketype
[Fe2S2] ferredoxin.
In benzoate and toluate 1,2dioxygenase systems, a single protein
containing reductase and Riesketype ferredoxin domains transfers the
electrons from NADH to the hydroxylase component
[1].
In the phthalate 4,5dioxygenase system, phthalate dioxygenase reductase
(PDR) has the same function. PDR is a single protein comprising
FMNbinding reductase and planttype
ferredoxin domains.
Thus, the electron transfer in ARHD systems can be summarised as (3)
(see also electron transfer chains in ARHD systems):
FAD or FMN
[Fe2S2] subunit
[Fe2S2], Fe(3)
ß)3
hexamer. The ß subunit belongs to the
+ß class. It has no prosthetic
groups and its role in catalysis is unknown.
The subunit can be divided
into two domains: a Rieske domain that contains the
[Fe2S2] centre and the catalytic domain that contains the
active site mononuclear iron. The Rieske domain (residues 38-158) consists of
four ßsheets. The overall fold is very similar to that of the
soluble fragment of the Rieske protein from bovine
heart mitochondrial
cytochrome bc1 complex.
In the [Fe2S2] centre, Fe1 is coordinated by
Cys81 and Cys101 while Fe2 is coordinated by
NHis atoms of
His83 and His104.
The catalytic domain belongs to the
+ß class and is dominated by a
ninestranded antiparallel ßsheet. The iron of the active site
is located at the bottom of a narrow channel, approximately 15 Å from the
protein surface. The mononuclear iron is
coordinated by His208, His213, Asp362 (bidentate) and a water
molecule. The geometry can be described as a distorted octahedral with one
ligand missing.
The structure of the hexamer suggests cooperativity between adjacent
subunits, where electrons from the
[Fe2S2] centre in one
subunit (A) are transferred to the
mononuclear iron in the adjacent
subunit (B) through AspB205, which is hydrogen bonded to
HisA104 of the Rieske centre and HisB208 of
the active site.
Electron transfer chains in ARHD systems
| System | Electron transfer chain | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Pseudomonas putida benzene 1,2dioxygenase |
|
||||||||||
| Pseudomonas putida benzene 1,2dioxygenase |
|
||||||||||
| Pseudomonas putida naphthalene 1,2dioxygenase |
|
||||||||||
| Pseudomonas putida toluene 2,3dioxygenase |
|
||||||||||
| Burkholderia cepacia biphenyl dioxygenase |
|
||||||||||
| Pseudomonas putida toluate 1,2dioxygenase |
|
||||||||||
| Acinetobacter sp. ADP1 benzoate 1,2dioxygenase |
|
||||||||||
| Burkholderia cepacia phthalate 4,5dioxygenase |
|
||||||||||
| ENZYME | LIGAND | BRENDA | UMBBD | Official name | Alternative names |
|---|---|---|---|---|---|
| 1.14.12.3 | 1.14.12.3 | 1.14.12.3 | e0059 | Benzene 1,2dioxygenase | Benzene hydroxylase |
| 1.14.12.7 | 1.14.12.7 | 1.14.12.7 | e0104 | Phthalate 4,5dioxygenase | |
| 1.14.12.8 | 1.14.12.8 | 1.14.12.8 | e0128 | 4Sulphobenzoate 3,4dioxygenase | |
| 1.14.12.9 | 1.14.12.9 | 1.14.12.9 | e0290 | 4Chlorophenylacetate 3,4dioxygenase | |
| 1.14.12.10 | 1.14.12.10 | 1.14.12.10 | e0154 | Benzoate 1,2dioxygenase | Benzoate hydroxylase |
| 1.14.12.11 | 1.14.12.11 | 1.14.12.11 | e0155 | Toluene 1,2dioxygenase | Toluene hydroxylase |
| 1.14.12.12 | 1.14.12.12 | 1.14.12.12 | e0002 | Naphthalene 1,2dioxygenase | |
| 1.14.12.15 | 1.14.12.15 | e0107 | Terephthalate 3,4dioxygenase | Benzene1,4dicarboxylate 1,2dioxygenase; 1,4dicarboxybenzoate 1,2dioxygenase. | |
| 1.14.12.- | 1.14.12.- | 1.14.12.- | e0030 | Dibenzofuran 4,4adioxygenase | |
| 1.14.12.- | 1.14.12.- | 1.14.12.- | e0160 | Dibenzothiophene 1,2dioxygenase | |
| 1.14.12.- | 1.14.12.- | 1.14.12.- | e0190 | Toluate 1,2dioxygenase | |
| 1.14.12.- | 1.14.12.- | 1.14.12.- | e0217 | Ethylbenzene 2,3dioxygenase | |
| 1.14.99.- | 1.14.99.- | 1.14.12.- | e0089 | Biphenyl dioxygenase | |
| PRINTS ID | PRINTS AC | PROSITE/BLOCKS ID | PROSITE AC | BLOCKS AC |
|---|---|---|---|---|
| RNGDIOXGNASE | PR00090 | RING_HYDROXYL_ALPHA | PS00570 | BL00570 |
| Protein (Super)family | Pfam | LPFC 3D alignment |
|---|---|---|
|
00189;
toluene dioxygenase terminal oxygenase component large chain
11870; benzoate 1,2dioxygenase |
References
subunit of toluene dioxygenase:
Potential mononuclear nonheme iron coordination sites.
J. Bacteriol. 178, 3133-3139.
| Bibliography on structural studies of aromaticringhydroxylating dioxygenases |
2O