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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 M0242 and M0300

These two reactions have a combined similarity of 0.53


M0242

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Comparison

M0300

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EC 3.1.4.41
sphingomyelin phosphodiesterase D
Serial Number EC 3.1.4.46
glycerophosphodiester phosphodiesterase

Image of water

Image of Sphingomyelin

right arrow

Image of Ceramide 1-phosphate

Image of Choline

water
C00001
CHEBI:15377
Sphingomyelin
C00550
CHEBI:58216
Ceramide 1-phosphate
C02960
Choline
C00114
CHEBI:15354
1

Image of water

Image of glycerophosphodiester

right arrow

Image of sn-Glycerol 3-phosphate

Image of alcohol

water
C00001
CHEBI:15377
glycerophosphodiester
C03120
sn-Glycerol 3-phosphate
C00093
CHEBI:15978
alcohol
C00069
CHEBI:30879

Catalytic CATH Codes

3.20.20.190

Catalytic CATH Codes

3.20.20.190

Active Site



0.488

Active Site



Catalytic Residues

Type Number Chain Location of Function
His 47 A Side Chain
His 12 A Side Chain
Gly 48 A Main Chain Carbonyl
Asp 34 A Side Chain
Asn 252 A Side Chain
Asp 233 A Side Chain
Asp 52 A Side Chain
Trp 230 A Side Chain
Lys 93 A Side Chain
0.5

Catalytic Residues

Type Number Chain Location of Function
Asp 239 A Side Chain
His 17 A Side Chain
His 59 A Side Chain
Arg 18 A Side Chain
Lys 121 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
magnesium MG 601 _

Metal Cofactors

Type Het group Number Chain
magnesium CA 502 B

Reaction occurs across 4 steps

0.4782

Reaction occurs across 2 steps

Step 1
GIF of Reaction Step M0242.stg01

His47 is the nucleophile for attack on the phosphorous of the scissile phosphodiester. A penta-coordinated intermediate is formed.
0 Step 1
GIF of Reaction Step M0300.stg01

His17 deprotonates the substrate alcohol, which initiates a nucleophilic attack on the phosphate group, eliminating the product alcohol with concomitant deprotonation of His59
Step 2
GIF of Reaction Step M0242.stg02

The intermediate collapses and eliminates choline, which is protonated by His12.
0.5 Step 2
GIF of Reaction Step M0300.stg02

His59 deprotonates water, which initiates a nucleophilic attack on the phosphate group, destroying the cyclic intermediate with concomitant deprotonation of His17
Step 3
GIF of Reaction Step M0242.stg03

His12 deprotonates water, which then acts as the nucleophile for attack on the phosphorous centre of the intermediate. A penta-coordinated intermediate is formed.
N/A Step 3
No Step with this number present
Step 4
GIF of Reaction Step M0242.stg04

The intermediate collapses and eliminates His47. This forms ceramide 1-phosphate.
N/A Step 4
No Step with this number present

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