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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 M0089 and M0259

These two reactions have a combined similarity of 0.45


M0089

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Comparison

M0259

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EC 4.2.3.7
pentalenene synthase
Class EC 5.5.1.8
bornyl diphosphate synthase

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
0.48

Image of geranyl diphosphate

right arrow

Image of (+)-bornyl diphosphate

geranyl diphosphate
C00341
CHEBI:58057
(+)-bornyl diphosphate
C03190
CHEBI:57293

Catalytic CATH Codes

1.10.600.10

Catalytic CATH Codes

1.10.600.10

Active Site



0.3375

Active Site



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
0.375

Catalytic Residues

Type Number Chain Location of Function
Trp 323 A Side Chain
Phe 578 A Side Chain
Ile 344 A Side Chain
Val 452 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

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

Metal Cofactors

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

Reaction occurs across 7 steps

0.4909

Reaction occurs across 6 steps

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.
1 Step 1
GIF of Reaction Step M0259.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 M0089.stg02

The terminal double bond adds to the terminal carbocation in an intramolecular electrophilic addition resulting in a cyclic intermediate.
0.25 Step 2
GIF of Reaction Step M0259.stg02

The diphosphate initiates nucleophilic attack at the C4 carbon, which causes double bond rearrangement and the formation of the linalyl diphosphate intermediate.
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.
0 Step 3
GIF of Reaction Step M0259.stg03

The linalyl diphosphate 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 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.
0.62 Step 4
GIF of Reaction Step M0259.stg04

The terminal double bond adds to the newly formed carbocation in an intramolecular electrophilic addition resulting in a cyclic intermediate.
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
0.5 Step 5
GIF of Reaction Step M0259.stg05

The remaining double bond adds to the newly formed carbocation in an intramolecular electrophilic addition resulting in a bicyclic intermediate.
Step 6
GIF of Reaction Step M0089.stg06

His309 deprotonates the carbon adjacent to the new carbocation, forming the final double bond of pentalenene.
0 Step 6
GIF of Reaction Step M0259.stg06

The diphosphate initiates nucleophilic attack at the carbocation, forming the final product.
Step 7
GIF of Reaction Step M0089.stg07

Water deprotonates His309 in an inferred step to regenerate the enzyme active site.
N/A Step 7
No Step with this number present

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