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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 M0270 and M0267

These two reactions have a combined similarity of 0.14


M0270

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Comparison

M0267

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EC 5.1.3.1
ribulose-phosphate 3-epimerase
Class EC 4.2.1.52
dihydrodipicolinate synthase

Image of D-Ribulose 5-phosphate

right arrow

Image of D-Xylulose 5-phosphate

D-Ribulose 5-phosphate
C00199
CHEBI:17363
D-Xylulose 5-phosphate
C00231
CHEBI:16332
0

Image of L-aspartate beta semi aldehyde (hydrate)

Image of Pyruvate

right arrow

Image of (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid

Image of water

L-aspartate beta semi aldehyde (hydrate)
X00125
Pyruvate
C00022
CHEBI:15361
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid
X00126
2 water
C00001
CHEBI:15377

Catalytic CATH Codes

3.20.20.70

Catalytic CATH Codes

3.20.20.70

Active Site



0.0148

Active Site



Catalytic Residues

Type Number Chain Location of Function
Asp 178 A Side Chain
Asp 38 A Side Chain
Ser 11 A Side Chain
0

Catalytic Residues

Type Number Chain Location of Function
Lys 161 A Side Chain
Tyr 133 A Side Chain
Ile 203 A Main Chain Carbonyl

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
zinc ZN 1224 A

Metal Cofactors

No Associated Metal Cofactors

Reaction occurs across 3 steps

0.2187

Reaction occurs across 9 steps

Step 1
GIF of Reaction Step M0270.stg01

Asp38 deprotonates the C3 of the substrate molecule, causing a rearrangement of the double bonds and the formation of the enolate form.
0.2 Step 1
GIF of Reaction Step M0267.stg01

Lys161 acts as a nucleophile towards the keto group of the pyruvate substrate, forming a covalently bound enzyme-substrate intermediate. The pyruvate is polarised by the presence of the main chain carbonyl of Ile203, increasing its electrophilicity.
Step 2
GIF of Reaction Step M0270.stg02

The enolate collapses back to the keto form with concomitant deprotonation of Asp178, forming the xylulose product.
0 Step 2
GIF of Reaction Step M0267.stg02

Proton transfer activates Schiff base formation in the next reaction step.
Step 3
GIF of Reaction Step M0270.stg03

Bulk solvent returns the two catalytic aspartate residues to their correct protonation states.
0.33 Step 3
GIF of Reaction Step M0267.stg03

Elimination of water results in Schiff base formation.
Step 4
No Step with this number present
N/A Step 4
GIF of Reaction Step M0267.stg04

The covalently bound lysine abstracts a proton from the terminal carbon to form the ene tautomer.
Step 5
No Step with this number present
N/A Step 5
GIF of Reaction Step M0267.stg05

L-aspartate semi aldehyde is thought to enter the active site in the hydrate form. It then undergoes reversible dehydration to form the protonated aldehyde form.
Step 6
No Step with this number present
N/A Step 6
GIF of Reaction Step M0267.stg06

The enamine tautomer of the Schiff base adds to the dehydrated L-aspartate semi aldehyde in a conjugate nucleophilic attack.
Step 7
No Step with this number present
N/A Step 7
GIF of Reaction Step M0267.stg07

A 6-exo-tet cyclisation (Baldwin's classification) occurs in the enzyme-substrate intermediate.
Step 8
No Step with this number present
N/A Step 8
GIF of Reaction Step M0267.stg08

Proton transfer is mediated through Tyr133.
Step 9
No Step with this number present
N/A Step 9
GIF of Reaction Step M0267.stg09

The product is formed and the active site is regenerated for further catalysis.

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