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The two reactions compared are done so using a Tanimoto similarity score (for more information, please see the MACiE FAQ) for the bond changes only. The score maay range from 0 to 1 where 1 indicates that the two reactions are identical at the bond change level and 0 indicates that there are no bond changes in common.


Key

1.0-0.9 0.9-0.8 0.8-0.7 0.7-0.6 0.6-0.5 0.5-0.4 0.4-0.3 0.3-0.2 0.2-0.1 0.1-0.0 =0

Results for Comparison of M0208 and M0130

These two reactions have a combined similarity of 0.28


M0208

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Comparison

M0130

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EC 1.10.2.2
ubiquinol-cytochrome-c reductase
Sub-Class EC 1.14.12.12
naphthalene 1,2-dioxygenase

Image of Ubiquinone

Image of Ubiquinol

Image of Ferricytochrome c

right arrow

Image of Ubiquinone

Image of Proton

Image of Ubiquinol

Image of Ferrocytochrome c

Ubiquinone
C00399
CHEBI:16389
2 Ubiquinol
C00390
CHEBI:17976
2 Ferricytochrome c
C00125
CHEBI:15991
2 Ubiquinone
C00399
CHEBI:16389
2 Proton
C00080
CHEBI:24636
Ubiquinol
C00390
CHEBI:17976
2 Ferrocytochrome c
C00126
CHEBI:16928
0.20

Image of naphthalene

Image of oxygen

Image of proton

Image of NADH

right arrow

Image of NAD

Image of cis-1,2-dihydronaphthalene-1,2-diol

naphthalene
C00829
CHEBI:16482
oxygen
C00007
CHEBI:15379
proton
C00080
CHEBI:24636
NADH
C00004
CHEBI:16908
NAD
C00003
CHEBI:15846
cis-1,2-dihydronaphthalene-1,2-diol
C04314
CHEBI:15561

Catalytic CATH Codes

1.20.810.10
2.102.10.10

Catalytic CATH Codes

2.102.10.10
3.90.380.10

Active Site



0.5625

Active Site



Catalytic Residues

Type Number Chain Location of Function
His 161 E Side Chain
Glu 272 C Side Chain
His 202 C Side Chain
Lys 228 C Side Chain
Asp 229 C Side Chain
Ser 206 C Side Chain
0.625

Catalytic Residues

Type Number Chain Location of Function
His 104 A Side Chain
Asp 205 E Side Chain
His 208 E Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

Type Identity Chain
FAD FAD 0

Metal Cofactors

Type Het group Number Chain
iron HEM 401 C
iron HEM 402 C
iron HEM 3 D
iron FES 4 E

Metal Cofactors

Type Het group Number Chain
iron FES 451 A
iron FE 452 A
iron FE(not in PDB) 1 x
iron FE(not in PDB) 2 x

Reaction occurs across 7 steps

0.1935

Reaction occurs across 9 steps

Step 1
GIF of Reaction Step M0208.stg01

Glu272 deprotonates the quinol substrate. His161 (bound to a Rieske iron-sulfur cluster) deprotonates the second alcohol group. This initiates a single electron transfer to the Rieske iron-sulfur cluster forming the semi-quinone intermediate.
0.05 Step 1
GIF of Reaction Step M0130.stg01

NAD initiates a hydride transfer to the FAD cofactor.
Step 2
GIF of Reaction Step M0208.stg02

The alkoxide of the semi-quinone intermediate initiates a second single electron transfer (forming the first quinone product) through two heme groups to the quinone substrate, which initiates double bond rearrangement generating a semi-quinone intermediate
0.12 Step 2
GIF of Reaction Step M0130.stg02

FAD undergoes a double bond rearrangement that results in the transfer of a single electron from the FAD to one of the iron-sulfur clusters. This then initiates an electron relay through a second iron-sulfur cluster to a third.
Step 3
GIF of Reaction Step M0208.stg03

Water deprotonates His161, which initiates a single electron transfer from the Rieske iron-sulfur complex to the heme group of cytochrome-c1. Concurrently, water deprotonates Glu272.
0.41 Step 3
GIF of Reaction Step M0130.stg03

The electron is transferred from the final iron-sulfur cluster to a dioxygen molecule, which also accepts a second electron from another Fe(II) centre, and deprotonates a water molecule.
Step 4
GIF of Reaction Step M0208.stg04

Glu272 deprotonates the second quinol substrate. His161 (bound to a Rieske iron-sulfur cluster) deprotonates the second alcohol group. This initiates a single electron transfer to the Rieske iron-sulfur cluster forming the semi-quinone intermediate.
0 Step 4
GIF of Reaction Step M0130.stg04

The peroxo group attacks the naphthalene substrate in a nucleophilic addition that causes the double bond to attack the peroxo group, cleaving the O-O bond and forming the epoxide intermediate.
Step 5
GIF of Reaction Step M0208.stg05

The alkoxide of the second semi-quinone intermediate initiates a second single electron transfer (forming the second quinone product) through two heme groups to the semi-quinone substrate, which initiates double bond rearrangement generating the quinol product, that deprotonates Lys228 through a water molecule.
0 Step 5
GIF of Reaction Step M0130.stg05

The epoxide intermediate collapses in a heterolysis resulting in a carbocation and anioinc oxygen bound to the Fe(III) centre.
Step 6
GIF of Reaction Step M0208.stg06

Water deprotonates His161, which initiates a single electron transfer from the Rieske iron-sulfur complex to the heme group of cytochrome-c1. Concurrently, water deprotonates Glu272.
0 Step 6
GIF of Reaction Step M0130.stg06

The iron-bound hydroxide group attacks the carbocation in a coordination reaction.
Step 7
GIF of Reaction Step M0208.stg07

Lys228 deprotonates water.
0 Step 7
GIF of Reaction Step M0130.stg07

An unidentified base deprotonates the FAD, initiating a single electron transfer to the one of the iron-sulfur clusters. This then initiates an electron relay through a second iron-sulfur cluster to a third.
Step 8
No Step with this number present
N/A Step 8
GIF of Reaction Step M0130.stg08

The electron is transferred from the final iron-sulfur cluster to the Fe(III) centre
Step 9
No Step with this number present
N/A Step 9
GIF of Reaction Step M0130.stg09

The cis-1,2-dihydronaphthalene-1,2-diol product deprotonates a water molecule and de-coordinates from the Fe(II) centre.

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