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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 M0229 and M0235

These two reactions have a combined similarity of 0.51


M0229

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Comparison

M0235

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EC 6.3.2.1
pantoate-beta-alanine ligase
Sub-Class EC 6.1.1.19
arginine-tRNA ligase

Image of beta-Alanine

Image of ATP

Image of (R)-Pantoate

right arrow

Image of Pantothenate

Image of AMP

Image of diphosphate

beta-Alanine
C00099
CHEBI:57966
ATP
C00002
CHEBI:30616
(R)-Pantoate
C00522
CHEBI:15980
Pantothenate
C00864
CHEBI:29032
AMP
C00020
CHEBI:456215
diphosphate
C00013
CHEBI:33019
0.38

Image of L-Arginine

Image of ATP

Image of tRNA(Arg)

right arrow

Image of L-Arginyl-tRNA(Arg)

Image of AMP

Image of diphosphate

L-Arginine
C00062
CHEBI:32682
ATP
C00002
CHEBI:30616
tRNA(Arg)
C01636
CHEBI:29171
L-Arginyl-tRNA(Arg)
C02163
CHEBI:18366
AMP
C00020
CHEBI:456215
diphosphate
C00013
CHEBI:18361

Catalytic CATH Codes

3.40.50.620
3.30.1300.10

Catalytic CATH Codes

3.40.50.620

Active Site



0.3892

Active Site



Catalytic Residues

Type Number Chain Location of Function
His 44 A Side Chain
His 47 A Side Chain
Ser 196 A Side Chain
Ser 197 A Side Chain
Arg 198 A Side Chain
0.4

Catalytic Residues

Type Number Chain Location of Function
His 159 A Side Chain
Lys 156 A Side Chain
His 162 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
magnesium MG 1001 _

Metal Cofactors

Type Het group Number Chain
magnesium No Available PDB Information

Reaction occurs across 5 steps

0.5789

Reaction occurs across 3 steps

Step 1
GIF of Reaction Step M0229.stg01

The carboxylate oxygen is involved in in-line nucleophilic attack on the alpha-phosphate of ATP to produce pyrophosphate and a pantoyl adenylate intermediate. The pyrophosphate is protonated by His147.
0.5 Step 1
GIF of Reaction Step M0235.stg01

The carboxylate oxygen of arginine is the nucleophile for in-line displacement at the alpha-phosphate of ATP. This produces pyrophosphate and an arginyl-adenylate intermediate.
Step 2
GIF of Reaction Step M0229.stg02

The phosphate group of the pantoyl adenylate forms a hydrogen-bond with the amine group of the beta-alanine substrate, deprotonating it to make the beta-alanine a better nucleophile
0.2 Step 2
GIF of Reaction Step M0235.stg02

The 2'-hydroxyl of the 3'-terminal adenosine of the tRNA molecule is the nucleophile for attack on the carbonyl carbon of the arginyl-adenylate intermediate. This forms a tetrahedral intermediate.
Step 3
GIF of Reaction Step M0229.stg03

Beta-alanine initiates a nucleophilic attack on the carbonyl of the pantoyl adenylate intermediate to form a tetrahedral intermediate.
0 Step 3
GIF of Reaction Step M0235.stg03

The tetrahedral intermediate collapses and eliminates AMP to form L-arginyl-tRNA.
Step 4
GIF of Reaction Step M0229.stg04

The tetrahedral intermediate collapses to eliminate AMP and the product, pantothenate, which almost immediately dissociates from the active site.
N/A Step 4
No Step with this number present
Step 5
GIF of Reaction Step M0229.stg05

His47 deprotonates water in an inferred return step.
N/A Step 5
No Step with this number present

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