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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 M0011 and M0308

These two reactions have a combined similarity of 0.08


M0011

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Comparison

M0308

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EC 3.1.21.2
deoxyribonuclease IV (phage-T4-induced)
Class EC 5.3.1.5
xylose isomerase

Image of DNA

Image of water

right arrow

Image of DNA 5'-phosphate

Image of DNA 3'-hydroxyl

DNA
C00039
CHEBI:9160
water
C00001
CHEBI:15377
DNA 5'-phosphate
X00015
DNA 3'-hydroxyl
X00016
0

Image of D-xylose

right arrow

Image of D-xylulose

D-xylose
C00181
CHEBI:53455
D-xylulose
C00310
CHEBI:17140

Catalytic CATH Codes

3.20.20.150

Catalytic CATH Codes

3.20.20.150

Active Site



0.0258

Active Site



Catalytic Residues

Type Number Chain Location of Function
Glu 261 A Side Chain
0

Catalytic Residues

Type Number Chain Location of Function
Met 83 A Side Chain
Asp 292 A Side Chain
Lys 182 A Side Chain
Asp 56 A Side Chain
His 53 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
zinc ZN 301 x
zinc ZN 302 x
zinc ZN 303 x

Metal Cofactors

Type Het group Number Chain
manganese MN 398 A
manganese MN 399 A

Reaction occurs across 2 steps

0.1282

Reaction occurs across 5 steps

Step 1
GIF of Reaction Step M0011.stg01

Zinc activated water initiates a nucleophilic attack on the DNA phosphate, concomitantly eliminating the 5'-ribose in a substitution reaction which proceeds through a pentavalent transition state.
0 Step 1
GIF of Reaction Step M0308.stg01

D-xylose undergoes a catalysed ring opening reaction.
Step 2
GIF of Reaction Step M0011.stg02

The DNA 3'-hydroxyl deprotonates a water molecule to regenerate the zinc activated hydroxide and the 3'hydroxyl product in an inferred return step.
1 Step 2
GIF of Reaction Step M0308.stg02

Asp292A deprotonates the water coordinated to the second Mg cofactor (MG399A), forming a hydroxide.
Step 3
No Step with this number present
N/A Step 3
GIF of Reaction Step M0308.stg03

An intramolecular 1,2 hydride transfer mechanism occurs, involving a hydroxide anion base and a divalent, cationic metal cofactor.
Step 4
No Step with this number present
N/A Step 4
GIF of Reaction Step M0308.stg04

The sugar now undergoes catalysed ring closure by the reverse mechanism of ring opening.
Step 5
No Step with this number present
N/A Step 5
GIF of Reaction Step M0308.stg05

The active site is regenerated by reprotonation of the hydroxide ligand to form water.

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