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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 M0264 and M0262

These two reactions have a combined similarity of 0.74


M0264

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Comparison

M0262

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EC 2.5.1.21
squalene synthase
Class EC 4.2.3.6
trichodiene synthase

Image of NADPH

Image of 2-trans,6-trans-farnesyl diphosphate

right arrow

Image of proton

Image of NADP

Image of squalene

Image of diphosphate

NADPH
C00005
CHEBI:16908
2 2-trans,6-trans-farnesyl diphosphate
C00448
CHEBI:175763
proton
C00080
CHEBI:24636
NADP
C00006
CHEBI:15846
squalene
C00751
CHEBI:15440
2 diphosphate
C00013
CHEBI:33019
0.5

Image of 2-trans,6-trans-farnesyl diphosphate

right arrow

Image of trichodiene

Image of diphosphate

2-trans,6-trans-farnesyl diphosphate
C00448
CHEBI:175763
trichodiene
C01860
CHEBI:15861
diphosphate
C00013
CHEBI:33019

Catalytic CATH Codes

1.10.600.10

Catalytic CATH Codes

1.10.600.10

Active Site



0.4615

Active Site



Catalytic Residues

Type Number Chain Location of Function
Tyr 171 A Side Chain
Arg 228 A Side Chain
Arg 218 A Side Chain
Phe 288 A Side Chain
0.5

Catalytic Residues

Type Number Chain Location of Function
Tyr 93 B Side Chain
Arg 182 B Side Chain
Lys 232 B Side Chain
Arg 304 B Side Chain
Tyr 305 B Side Chain
Thr 96 B Side Chain
Leu 97 B Side Chain
Asp 100 B Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
magnesium No Available PDB Information
magnesium No Available PDB Information
magnesium No Available PDB Information

Metal Cofactors

Type Het group Number Chain
magnesium MG 701 B
magnesium MG 702 B
magnesium MG 703 B

Reaction occurs across 7 steps

0.8867

Reaction occurs across 6 steps

Step 1
GIF of Reaction Step M0264.stg01

Pyrophosphate is eliminated with concomitant deprotonation of Tyr171.
0.6 Step 1
GIF of Reaction Step M0262.stg01

The binding of the substrate causes a conformation change in the active site, which promotes the elimination of the pyrophosphate.
Step 2
GIF of Reaction Step M0264.stg02

The second molecule of farnesyl diphosphate initiates an electrophilic attack on the intermediate formed.
0 Step 2
GIF of Reaction Step M0262.stg02

The pyrophosphate attacks the C3 cationic carbon in a nucleophilic addition reaction.
Step 3
GIF of Reaction Step M0264.stg03

Tyr171 acts as a base to deprotonate the intermediate, forming the stable intermediate presqualene diphosphate, the product of the first half reaction.
0 Step 3
GIF of Reaction Step M0262.stg03

Intramolecular elimination of the pyrophosphate.
Step 4
GIF of Reaction Step M0264.stg04

The substrate undergoes heterolysis.
0 Step 4
GIF of Reaction Step M0262.stg04

Intramolecular electrophilic addition across the C1-C6 bond to form the six-membered ring.
Step 5
GIF of Reaction Step M0264.stg05

A 1,2 sigmatropic rearrangement to produce the cyclobutyl intermediate.
0.33 Step 5
GIF of Reaction Step M0262.stg05

Intramolecular electrophilic addition across the C10-C7 bond to form the five-membered ring.
Step 6
GIF of Reaction Step M0264.stg06

A 1,2 sigmatropic rearrangement to produce the second cyclopropyl intermediate.
0.30 Step 6
GIF of Reaction Step M0262.stg06

The Pyrophosphate deprotonates the substrate, which initiates the first methyl migration, followed by a second methyl migration and finally a 1,4-hydride shift.
Step 7
GIF of Reaction Step M0264.stg07

A hydride transfer from NADP caused the cleavage of the cyclopropyl group to produce squalene.
N/A Step 7
No Step with this number present

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