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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 M0262 and M0089

These two reactions have a combined similarity of 0.50


M0262

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Comparison

M0089

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EC 4.2.3.6
trichodiene synthase
Serial Number EC 4.2.3.7
pentalenene synthase

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
0.76

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

right arrow

Image of proton

Image of pentalenene

Image of diphosphate

2-trans,6-trans-farnesyl diphosphate
C00448
CHEBI:175763
proton
C00080
CHEBI:24636
pentalenene
C01841
CHEBI:17251
diphosphate
C00013
CHEBI:18361

Catalytic CATH Codes

1.10.600.10

Catalytic CATH Codes

1.10.600.10

Active Site



0.0097

Active Site



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
0

Catalytic Residues

Type Number Chain Location of Function
Phe 76 A Side Chain
Phe 77 A Side Chain
Asn 219 A Side Chain
Trp 308 A Side Chain
His 309 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

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

Metal Cofactors

Type Het group Number Chain
magnesium MG(not in PDB) 1 x

Reaction occurs across 6 steps

0.6551

Reaction occurs across 7 steps

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.
0.33 Step 1
GIF of Reaction Step M0089.stg01

The substrate undergoes heterolysis. The diphosphate product remains associated with the active site, and the cabocation is delocalised over the three terminal carbon atoms of the intermediate.
Step 2
GIF of Reaction Step M0262.stg02

The pyrophosphate attacks the C3 cationic carbon in a nucleophilic addition reaction.
0 Step 2
GIF of Reaction Step M0089.stg02

The terminal double bond adds to the terminal carbocation in an intramolecular electrophilic addition resulting in a cyclic intermediate.
Step 3
GIF of Reaction Step M0262.stg03

Intramolecular elimination of the pyrophosphate.
0.2 Step 3
GIF of Reaction Step M0089.stg03

His309 deprotonates the carbon adjacent to the newly formed carbocation, forming a new double bond in the humulene intermediate.
Step 4
GIF of Reaction Step M0262.stg04

Intramolecular electrophilic addition across the C1-C6 bond to form the six-membered ring.
0.5 Step 4
GIF of Reaction Step M0089.stg04

In a second intramolecular electrophilic addition, a double bond adds across the cycle forming a five membered ring and a new carbocation.
Step 5
GIF of Reaction Step M0262.stg05

Intramolecular electrophilic addition across the C10-C7 bond to form the five-membered ring.
0.5 Step 5
GIF of Reaction Step M0089.stg05

In a third intramolecular electrophilic addition, the remaining double bond adds across the cycle to form the three five membered ring motif of pentalenene, this also causes a [1,2]-hydride shift and the carbocation shifting to a different carbon atom
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.
0.2 Step 6
GIF of Reaction Step M0089.stg06

His309 deprotonates the carbon adjacent to the new carbocation, forming the final double bond of pentalenene.
Step 7
No Step with this number present
N/A Step 7
GIF of Reaction Step M0089.stg07

Water deprotonates His309 in an inferred step to regenerate the enzyme active site.

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