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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 M0207 and M0272

These two reactions have a combined similarity of 0.19


M0207

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Comparison

M0272

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EC 2.7.9.1
pyruvate, phosphate dikinase
Class EC 4.1.3.1
isocitrate lyase

Image of phosphate

Image of ATP

Image of Pyruvate

right arrow

Image of Proton

Image of AMP

Image of Phosphoenolpyruvate

Image of diphosphate

phosphate
C00009
CHEBI:18367
ATP
C00002
CHEBI:15422
Pyruvate
C00022
CHEBI:15361
Proton
C00080
CHEBI:24636
AMP
C00020
CHEBI:456215
Phosphoenolpyruvate
C00074
CHEBI:58702
diphosphate
C00013
CHEBI:33019
0.15

Image of Glyoxylate

Image of Succinate

right arrow

Image of Isocitrate

Glyoxylate
C00048
CHEBI:36655
Succinate
C00042
CHEBI:30031
Isocitrate
C00311
CHEBI:16087

Catalytic CATH Codes

3.30.1490.20
3.50.30.10
3.20.20.60
3.30.470.20

Catalytic CATH Codes

3.20.20.60

Active Site



0.45

Active Site



Catalytic Residues

Type Number Chain Location of Function
Arg 92 A Side Chain
Lys 22 A Side Chain
His 455 A Side Chain
Arg 337 A Side Chain
Met 103 A Main Chain Amide
Gly 101 A Main Chain Amide
Tyr 851 A Side Chain
Ser 764 A Side Chain
Cys 831 A Side Chain
0.5

Catalytic Residues

Type Number Chain Location of Function
Ser 315 A Side Chain
Ser 317 A Side Chain
His 193 A Side Chain
Cys 191 A Side Chain
Arg 228 A Side Chain
His 180 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
magnesium MG(not in PDB) 2 x
magnesium MG 1001 A

Metal Cofactors

Type Het group Number Chain
magnesium MG 451 A

Reaction occurs across 3 steps

0.1041

Reaction occurs across 3 steps

Step 1
GIF of Reaction Step M0207.stg01

His455 attacks the beta phosphate of the ATP in a nucleophilic substitution that results in His455 carrying a pyrophosphate moiety and the AMP product.
0 Step 1
GIF of Reaction Step M0272.stg01

His193 deprotonates Cys191 which in turn deprotonates the alpha carbon of succinate to form the enolte.
Step 2
GIF of Reaction Step M0207.stg02

Free phosphate attacks the terminal phosphate of the His455 pyrophosphate moiety in a nuclephilic substitution, resulting in free pyrophosphate and phosphorylated His455.
0 Step 2
GIF of Reaction Step M0272.stg02

The intermedite reforms the keto form with concomitant addition to the glyoxylate substrate to form the product.
Step 3
GIF of Reaction Step M0207.stg03

In a proton relay chain involving bulk solvent, Tyr851, water, Ser764 and Cys831 the CH3 group of the pyruvate substrate is deprotonated. This initiates a double bond rearrangement that causes the ketone carbonyl group to attack the phosphorylated His455 in a nuclephilic substitution generating free His455 and the final product.
0.13 Step 3
GIF of Reaction Step M0272.stg03

In an inferred return step, the product deprotonates His193.

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