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Analysis of the 2-enoyl-CoA Hydratase; Chain A, domain 1 (CATH:3.90.226.10) dataset

There are 8 entries in this dataset.


Entry Number Enzyme Name EC Code PDB Code CATH Code
M0024
Structure Overview
4-chlorobenzoyl-CoA dehalogenase 3.8.1.7 1nzy 3.90.226.10
1.10.12.10
M0070
Structure Overview
methylmalonyl-CoA decarboxylase 4.1.1.41 1ef8 3.90.226.10
1.10.12.10
M0346
Structure Overview
1,4-dihydroxy-2-naphthoyl-CoA synthase 4.1.3.36 1q51 3.90.226.10
1.10.12.10
3.90.226.10
1.10.12.10
M0315
Structure Overview
enoyl-CoA hydratase 4.2.1.17 1ey3 3.90.226.10
1.10.12.10
3.90.226.10
M0343
Structure Overview
methylglutaconyl-CoA hydratase 4.2.1.18 1hzd 3.90.226.10
1.10.12.10
M0342
Structure Overview
delta(3,5)-delta(2,4)-dienoyl-CoA isomerase 5.3.3.- 1dci 3.90.226.10
1.10.12.10
M0341
Structure Overview
dodecenoyl-CoA isomerase 5.3.3.8 1sg4 3.90.226.10
3.90.226.10
M0201
Structure Overview
propionyl-CoA carboxylase 6.4.1.3 1xny 3.90.226.10

EC Class Composition

    


CATH Domain Composition

Step Analysis

There are an average of 3.12 number of steps in this dataset. The median number of steps is 2. The maximum number of steps in this dataset is 7 and the minimum is 1. The following graph shows the frequency of MACiE entries in this dataset with a given number of steps.


Amino Acid Residues

There are an average of 3.87 number of catalytic amino acid residues in a MACiE reaction for this dataset. The maximum number of amino acid residues in this dataset is 6 and the minimum is 3. The following barchart shows the frequency of the different catalytic amino acid residues in this dataset.


For the purposes of the following graph, amino acid residues are split into three generaic categories: polar (neutral), polar (charged) and hydrophobic. The neutral residues are: Ser, Thr, Cys, Asn, Gln, Tyr as well as the main chain portions of the amide and carbonyl groups. The charged residues are: Lys, Arg, His, Asp, Glu as well as the main chain portions of the N and C termini. The hydrophobic residues are: Ala, Val, Leu, Ile, Met, Phe, Trp, Pro, Gly. The following pie charts show the distribution of amino acid residue type by dataset (left) to the complete MACiE dataset (right)

    

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

Functional Profiles of the catalytic amino acids in 2-enoyl-CoA Hydratase; Chain A, domain 1 (CATH:3.90.226.10) Entries

Activation Steric Stabilisation Proton Shuttling Hydrogen Shuttling Single Electron Shuttling Electron Pair Shuttling Covalent Catalysis
Arg--------
Asn--------
Asp
(0.25)
0.33
0.08
-0.33
0.08
0.66
0.16
--0.33
0.08
0.33
0.08
Cys--------
Gln--------
Glu
(0.5)
0.16
0.08
--0.66
0.33
----
His
(0.12)
---1
0.12
----
Lys--------
Phe--------
Ser--------
Thr--------
Trp
(0.12)
--1
0.12
-----
Tyr
(0.25)
-1
0.25
0.66
0.16
0.33
0.08
----

The number below the residue name is the normalisation factor, and is calculated as the number of reactions in which that residue type occurs, divided by the total number of reactions in the dataset. The top number (emboldened) is the raw profile of that residue type and is calculated as the total number of unique residues of a given type performing a given function divided by the total number of that residue type in the dataset. The lower number is the normalised profile, which is calculated as the raw profile multiplied by the normalisation factor. Thus, if the residue is only ever seen in the dataset acting as a stabiliser, the raw profile will be 1, however, if that residue is only present in half the reactions, then the normailsation factor will be 0.5 and the normalised profile will also be 0.5.

Catalytic Machinery Similarities

This is calculated as a combination of the complement of catalytic amino acid residues present in each entry and the superimposition of the active site as calculated using IsoCleft.


M0024
3.8.1.7
M0070
4.1.1.41
M0346
4.1.3.36
M0315
4.2.1.17
M0343
4.2.1.18
M0342
5.3.3.-
M0341
5.3.3.8
M0201
6.4.1.3
M0024
3.8.1.7
10.25710.16570.180.20240.19990.13250.2999
M0070
4.1.1.41
0.257110.54450.13250.135600.20650.27
M0346
4.1.3.36
0.16570.544510.16610.149900.22250.4796
M0315
4.2.1.17
0.180.13250.166110.91710.24830.50930.3249
M0343
4.2.1.18
0.20240.13560.14990.917110.24830.50360.3211
M0342
5.3.3.-
0.1999000.24830.248310.12850.0226
M0341
5.3.3.8
0.13250.20650.22250.50930.50360.128510.27
M0201
6.4.1.3
0.29990.270.47960.32490.32110.02260.271

Cofactors

Number of Metal Cofactors Number of Organic CofactorsBiotinMg(II)
M0024
3.8.1.7
M0070
4.1.1.41
M0346
4.1.3.36
M0315
4.2.1.17
M0343
4.2.1.18
M0342
5.3.3.-
M0341
5.3.3.8
M0201
6.4.1.3
1 1 11

Mechanisms

The following graphs show the distribution of mechanism class by dataset (left) to the complete MACiE dataset (right)

    

The following graphs show the distribution of mechanism type by dataset (left) to the complete MACiE dataset (right)

    


Bond Changes

Overall Reaction Overview

C-C
Formed
C-C
Cleaved
C-C
Stereo
C-C
1 to 2
C-C
2 to 1
C-Cl
Cleaved
C-H
Formed
C-H
Cleaved
C-H
Stereo
C-O
Formed
C-O
Cleaved
C-O
1 to 2
C-O
2 to 1
O-H
Formed
O-H
Cleaved
P-O
Formed
P-O
Cleaved
M0024
3.8.1.7
111
M0070
4.1.1.41
11111
M0346
4.1.3.36
123124
M0315
4.2.1.17
1111
M0343
4.2.1.18
1111
M0342
5.3.3.-
2211
M0341
5.3.3.8
1111
M0201
6.4.1.3
111111111

Overall Reaction (Bond only) Similarities

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

M0024
3.8.1.7
M0070
4.1.1.41
M0346
4.1.3.36
M0315
4.2.1.17
M0343
4.2.1.18
M0342
5.3.3.-
M0341
5.3.3.8
M0201
6.4.1.3
M0024
3.8.1.7
1000.40.4000.0909
M0070
4.1.1.41
0100.1250.1250.07140.1250.1666
M0346
4.1.3.36
001000.18420.1470.2571
M0315
4.2.1.17
0.40.1250110.27270.33330.0833
M0343
4.2.1.18
0.40.1250110.27270.33330.0833
M0342
5.3.3.-
00.07140.18420.27270.272710.750.0555
M0341
5.3.3.8
00.1250.1470.33330.33330.7510.0833
M0201
6.4.1.3
0.09090.16660.25710.08330.08330.05550.08331

View overall reaction images

Step Centric Overview

MACiE Id Total Number of Overall Bond Changes Total Number of Steps Total Number of Step Bond Changes Average Number of bond changes per step Total Number of Bonds Formed Total Number of Bonds Cleaved Total Number of Bonds Changed Order
M0024
3.8.1.7
3 4 24 6 6 6 12
M0070
4.1.1.41
5 2 8 4 1 2 5
M0346
4.1.3.36
13 5 26 5.2 8 8 10
M0315
4.2.1.17
4 2 10 5 3 2 5
M0343
4.2.1.18
4 2 10 5 3 2 5
M0342
5.3.3.-
6 1 6 6 1 1 4
M0341
5.3.3.8
4 2 10 5 2 2 6
M0201
6.4.1.3
9 7 30 4.28 6 6 18

C-C
Formed
C-C
Cleaved
C-C
1 to 2
C-C
2 to 1
C-Cl
Cleaved
C-H
Formed
C-H
Cleaved
C-N
Formed
C-N
Cleaved
C-N
1 to 2
C-N
2 to 1
C-O
Formed
C-O
Cleaved
C-O
1 to 2
C-O
2 to 1
H-Cl
Formed
N-H
Formed
N-H
Cleaved
O-H
Formed
O-H
Cleaved
P-O
Formed
P-O
Cleaved
R-H
Formed
R-H
Cleaved
M0024
3.8.1.7
441212212212
M0070
4.1.1.41
1111211
M0346
4.1.3.36
131312474
M0315
4.2.1.17
12111112
M0343
4.2.1.18
12111112
M0342
5.3.3.-
2211
M0341
5.3.3.8
22111111
M0201
6.4.1.3
111111221661111111

Composite Reaction (Bond only) Similarities

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

This measure of similarity is based off the sum of all the bond changes in all the steps involved in the reaction mechanism.


M0024
3.8.1.7
M0070
4.1.1.41
M0346
4.1.3.36
M0315
4.2.1.17
M0343
4.2.1.18
M0342
5.3.3.-
M0341
5.3.3.8
M0201
6.4.1.3
M0024
3.8.1.7
10.15550.26920.33330.33330.28570.28880.2967
M0070
4.1.1.41
0.155510.05490.33330.33330.1250.3750.1232
M0346
4.1.3.36
0.26920.054910.17640.17640.07690.22890.3278
M0315
4.2.1.17
0.33330.33330.1764110.46660.6250.1025
M0343
4.2.1.18
0.33330.33330.1764110.46660.6250.1025
M0342
5.3.3.-
0.28570.1250.07690.46660.466610.20.012
M0341
5.3.3.8
0.28880.3750.22890.6250.6250.210.1282
M0201
6.4.1.3
0.29670.12320.32780.10250.10250.0120.12821

Reaction Similarities

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

Combined Similarities

This measure of similarity is based off the overall reaction bond change (10%), the sum of all the bond changes in all the steps involved in the reaction mechanism (65%) plus the complement of catalytic residues (25%) to give an estimate of the total similarity between two reactions.


M0024
3.8.1.7
M0070
4.1.1.41
M0346
4.1.3.36
M0315
4.2.1.17
M0343
4.2.1.18
M0342
5.3.3.-
M0341
5.3.3.8
M0201
6.4.1.3
M0024
3.8.1.7
10.16530.21640.30160.30720.23560.22080.2769
M0070
4.1.1.41
0.165310.17180.26220.26300.08830.30780.1642
M0346
4.1.3.36
0.21640.171810.15610.15210.06840.21910.3586
M0315
4.2.1.17
0.30160.26220.156110.97920.39260.56690.1561
M0343
4.2.1.18
0.30720.26300.15210.979210.39260.56540.1552
M0342
5.3.3.-
0.23560.08830.06840.39260.392610.23710.019
M0341
5.3.3.8
0.22080.30780.21910.56690.56540.237110.1591
M0201
6.4.1.3
0.27690.16420.35860.15610.15520.0190.15911
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