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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 M0270 and M0230

These two reactions have a combined similarity of 0.11


M0270

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Comparison

M0230

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EC 5.1.3.1
ribulose-phosphate 3-epimerase
Class EC 4.2.1.24
porphobilinogen synthase

Image of D-Ribulose 5-phosphate

right arrow

Image of D-Xylulose 5-phosphate

D-Ribulose 5-phosphate
C00199
CHEBI:17363
D-Xylulose 5-phosphate
C00231
CHEBI:16332
0

Image of 5-aminolevulinate

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Image of porphobilinogen

Image of water

2 5-aminolevulinate
C00430
CHEBI:12109
porphobilinogen
C00931
CHEBI:17381
2 water
C00001
CHEBI:15377

Catalytic CATH Codes

3.20.20.70

Catalytic CATH Codes

3.20.20.70

Active Site



0.0186

Active Site



Catalytic Residues

Type Number Chain Location of Function
Asp 178 A Side Chain
Asp 38 A Side Chain
Ser 11 A Side Chain
0

Catalytic Residues

Type Number Chain Location of Function
Lys 205 A Side Chain
Lys 260 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
zinc ZN 1224 A

Metal Cofactors

Type Het group Number Chain
magnesium MG 1338 A
zinc No Available PDB Information

Reaction occurs across 3 steps

0.1675

Reaction occurs across 16 steps

Step 1
GIF of Reaction Step M0270.stg01

Asp38 deprotonates the C3 of the substrate molecule, causing a rearrangement of the double bonds and the formation of the enolate form.
0.2 Step 1
GIF of Reaction Step M0230.stg01

The zinc activated water deprotonates Lys260, activating it for the first step in Schiff base formation.
Step 2
GIF of Reaction Step M0270.stg02

The enolate collapses back to the keto form with concomitant deprotonation of Asp178, forming the xylulose product.
0 Step 2
GIF of Reaction Step M0230.stg02

Lys260 initiates a nucleophilic attack at the substrate's C4 carbonyl carbon in the first step of Schiff base formation.
Step 3
GIF of Reaction Step M0270.stg03

Bulk solvent returns the two catalytic aspartate residues to their correct protonation states.
0.5 Step 3
GIF of Reaction Step M0230.stg03

In a proton rearrangement, the newly formed oxyanion deprotonates the positively charged nitrogen of Lys260.
Step 4
No Step with this number present
N/A Step 4
GIF of Reaction Step M0230.stg04

The long pair of Lys260 initiates the elimination of the hydroxyl group as water, with the extra proton being donated by the zinc activated water.
Step 5
No Step with this number present
N/A Step 5
GIF of Reaction Step M0230.stg05

The zinc activated water deprotonates Lys205, activating it for the first step in Schiff base formation.
Step 6
No Step with this number present
N/A Step 6
GIF of Reaction Step M0230.stg06

Lys205 initiates a nucleophilic attack at the second substrate's C4 carbonyl carbon in the first step of Schiff base formation.
Step 7
No Step with this number present
N/A Step 7
GIF of Reaction Step M0230.stg07

In a proton rearrangement, the newly formed oxyanion deprotonates the positively charged nitrogen of Lys205.
Step 8
No Step with this number present
N/A Step 8
GIF of Reaction Step M0230.stg08

The long pair of Lys260 initiates the elimination of the hydroxyl group as water, with the extra proton being donated by the zinc activated water.
Step 9
No Step with this number present
N/A Step 9
GIF of Reaction Step M0230.stg09

Zinc activated water deprotonates the Lys205 bound intermediate at the C3 carbon, initiating a tautomerisation.
Step 10
No Step with this number present
N/A Step 10
GIF of Reaction Step M0230.stg10

The lone pair of Lys205 initiates a double bond rearrangement that results in a nucleophilic attack of the Lys205 bound intermediate upon the C4 carbonyl carbon of the Lys260 bound intermediate, forming the new C3-C4 double bond.
Step 11
No Step with this number present
N/A Step 11
GIF of Reaction Step M0230.stg11

The amine group of the Lys260 bound intermediate initiates an intramolecular nucleophilic attack upon the C4 of the Lys205 bound intermediate, which in turn deprotonates the zinc activated water.
Step 12
No Step with this number present
N/A Step 12
GIF of Reaction Step M0230.stg12

Zinc activated water deprotonates the intermediate, causing an elimination of Lys205.
Step 13
No Step with this number present
N/A Step 13
GIF of Reaction Step M0230.stg13

The covalently attached Lys260 deprotonates the zinc activated water.
Step 14
No Step with this number present
N/A Step 14
GIF of Reaction Step M0230.stg14

Zinc activated water deprotonates the intermediate, causing an elimination of Lys260.
Step 15
No Step with this number present
N/A Step 15
GIF of Reaction Step M0230.stg15

Lys260 deprotonates the intermediate causing a double bond rearrangement that results in the final, aromatic, product.
Step 16
No Step with this number present
N/A Step 16
GIF of Reaction Step M0230.stg16

Lys205 deprotonates the zinc activated water to regenerate the enzyme's starting state.

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