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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 M0240 and M0215

These two reactions have a combined similarity of 0.31


M0240

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Comparison

M0215

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EC 3.5.1.-
histone/protein deacetylase
Class EC 4.1.1.1
pyruvate decarboxylase

Image of Protein acetyllysine

Image of water

Image of NAD

right arrow

Image of Nicotinamide

Image of 2'-O-acetyl ADP-ribose

Image of Protein lysine

Protein acetyllysine
X00123
CHEBI:61930
water
C00001
CHEBI:15377
NAD
C00003
CHEBI:15846
Nicotinamide
C00153
CHEBI:17154
2'-O-acetyl ADP-ribose
X00124
Protein lysine
C02188
CHEBI:29970
0.10

Image of Pyruvate

right arrow

Image of Carbon dioxide

Image of Acetaldehyde

Pyruvate
C00022
CHEBI:15361
Carbon dioxide
C00011
CHEBI:16526
Acetaldehyde
C00084
CHEBI:15343

Catalytic CATH Codes

3.40.50.1220
3.30.1600.10

Catalytic CATH Codes

3.40.50.970

Active Site



0.25264

Active Site



Catalytic Residues

Type Number Chain Location of Function
His 135 A Side Chain
Arg 45 A Side Chain
Phe 44 A Main Chain Amide
Side Chain
Asp 43 A Main Chain Amide
Pro 42 A Main Chain Carbonyl
Asp 118 A Side Chain
Asn 116 A Side Chain
0.2666

Catalytic Residues

Type Number Chain Location of Function
Glu 51 B Side Chain
Gly 417 A Main Chain Carbonyl
Asp 28 B Side Chain
Glu 477 A Side Chain
His 114 B Side Chain
His 115 B Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

Type Identity Chain
Thiamine diphosphate TPP 557 A

Metal Cofactors

No Associated Metal Cofactors

Metal Cofactors

Type Het group Number Chain
magnesium MG 558 A

Reaction occurs across 7 steps

0.3664

Reaction occurs across 6 steps

Step 1
GIF of Reaction Step M0240.stg01

With the aid of nitrogen lone pair donation, the acetyl oxygen of acetyllysine is the nucleophile for nucleophilic attack on the C1' position of NAD+, resulting in a substitution reaction in which nicotinamide is the leaving group. This produces a 1'-O-alkylamidate intermediate.
0.09 Step 1
GIF of Reaction Step M0215.stg01

Glu51B deprotonates the thiamine diphosphate cofactor, which initiates double bond rearrangement that results in the deprotonation of the N=CH-S group, activating the cofactor.
Step 2
GIF of Reaction Step M0240.stg02

His135 deprotonates the 3'-hydroxyl of the 1'-O-alkylamidate intermediate, which then itself deprotonates the 2'-hydroxyl. The resulting alkoxide is the nucleophile for intramolecular nucleophilic attack on the acetyl carbon. This produces a 1',2'-cyclic intermediate.
0.38 Step 2
GIF of Reaction Step M0215.stg02

The carbanion of thiamine diphosphate attacks the carbonyl carbon of pyruvate in a nucleophilic addition that results in the cofactor undergoing double bond rearrangement that results in the deprotonation of Glu51B.
Step 3
GIF of Reaction Step M0240.stg03

His135 protonates the lysine nitrogen in the 1',2'-cyclic intermediate.
0 Step 3
GIF of Reaction Step M0215.stg03

Carbon dioxide eliminates from the covalently attached pyruvate intermediate. Thiamine diphosphate acts as an electron sink.
Step 4
GIF of Reaction Step M0240.stg04

Lysine dissociates from the 1',2'-cyclic intermediate.
0 Step 4
GIF of Reaction Step M0215.stg04

Thiamine diphosphate initiates a double bond rearrangement, which results in the intermediate deprotonating Asp28B, which in turn deprotonates His115B.
Step 5
GIF of Reaction Step M0240.stg05

Water, positioned and possibly activated by Asn116, attacks the carbocation.
0 Step 5
GIF of Reaction Step M0215.stg05

Glu51B deprotonates thiamine diphosphate, which initiates a double bond rearrangement, that deprotonates the hydroxide of the intermediate, and results in a reformation of the carbanionic activated cofactor and the acetaldehyde product.
Step 6
GIF of Reaction Step M0240.stg06

The product lysine deprotonates the positively-charged oxygen.
0.33 Step 6
GIF of Reaction Step M0215.stg06

His115B deprotonates water. The carbanion of the thiamine diphosphate cofactor deprotonates the adjacent amine, which initiates double bond rearrangement that results in the deprotonation of Glu51B.
Step 7
GIF of Reaction Step M0240.stg07

The ring of the intermediate is opened when the exocyclic hydroxyl forms a carbonyl, with elimination and subsequent protonation of the endocyclic O1'.
N/A Step 7
No Step with this number present

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