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Analysis of the FAD/NAD(P)-binding domain (CATH:3.50.50.60) dataset

There are 9 entries in this dataset.


Entry Number Enzyme Name EC Code PDB Code CATH Code
M0108
Structure Overview
2,4-dienoyl-CoA reductase (NADPH) 1.3.1.34 1ps9 3.20.20.70
3.40.50.720
3.50.50.60
M0294
Structure Overview
succinate dehydrogenase (ubiquinone) 1.3.5.1 1yq4 3.50.50.60
Unassigned
1.10.1060.10
1.20.5.540
1.20.58.100
3.10.20.30
1.20.1300.10
4.10.80.40
M0020
Structure Overview
succinate dehydrogenase 1.3.99.1 1qjd 3.90.700.10
3.50.50.60
Unassigned
1.10.1130.10
Unassigned>
M0113
Structure Overview
sarcosine oxidase 1.5.3.1 2gb0 3.50.50.60
3.30.9.10
3.30.9.10
3.50.50.60
M0114
Structure Overview
trimethylamine dehydrogenase 1.5.8.2 2tmd 3.20.20.70
3.50.50.60
3.40.50.720
M0006
Structure Overview
glutathione-disulfide reductase 1.8.1.7 2gh5 3.50.50.60
3.30.390.30
3.30.390.30
3.50.50.60
M0123
Structure Overview
adenylyl-sulfate reductase 1.8.99.2 1jnr 3.50.50.60
3.90.700.10
3.30.70.20
1.20.58.100
M0131
Structure Overview
4-hydroxybenzoate 3-monooxygenase 1.14.13.2 1doc 3.50.50.60
3.30.9.10
M0142
Structure Overview
ferredoxin-NADP+ reductase 1.18.1.2 1e6e 3.40.50.720
3.50.50.60
3.10.20.30

EC Class Composition

    


CATH Domain Composition

Step Analysis

There are an average of 5 number of steps in this dataset. The median number of steps is 6. The maximum number of steps in this dataset is 9 and the minimum is 3. 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 5.55 number of catalytic amino acid residues in a MACiE reaction for this dataset. The maximum number of amino acid residues in this dataset is 8 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 FAD/NAD(P)-binding domain (CATH:3.50.50.60) Entries

Activation Steric Stabilisation Proton Shuttling Hydrogen Shuttling Single Electron Shuttling Electron Pair Shuttling Covalent Catalysis
Arg
(0.44)
0.14
0.06
0.14
0.06
0.71
0.31
0.42
0.18
----
Asn
(0.11)
1
0.11
-1
0.11
-----
Asp
(0.22)
0.5
0.11
-0.5
0.11
-----
Cys
(0.33)
0.5
0.16
--0.25
0.08
---0.5
0.16
Gln
(0.22)
-0.5
0.11
0.5
0.11
--0.5
0.11
--
Glu
(0.55)
0.33
0.18
0.16
0.09
0.66
0.36
0.16
0.09
----
His
(1)
0.09
0.09
0.18
0.18
0.54
0.54
0.36
0.36
----
Lys
(0.33)
-0.25
0.08
0.75
0.24
0.25
0.08
----
Phe
(0.11)
-1
0.11
------
Ser
(0.11)
--1
0.11
-----
Thr
(0.11)
---1
0.11
----
Trp
(0.11)
0.5
0.05
----0.5
0.05
--
Tyr
(0.33)
0.25
0.08
--0.75
0.24
----

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.


M0108
1.3.1.34
M0294
1.3.5.1
M0020
1.3.99.1
M0113
1.5.3.1
M0114
1.5.8.2
M0006
1.8.1.7
M0123
1.8.99.2
M0131
1.14.13.2
M0142
1.18.1.2
M0108
1.3.1.34
10.49860.41530.08180.32190.23780.2250.30980.1125
M0294
1.3.5.1
0.498610.68920.10580.13840.20980.26460.10580.1411
M0020
1.3.99.1
0.41530.689210.09460.11990.180.30450.09460.1194
M0113
1.5.3.1
0.08180.10580.094610.23790.38350.06210.25830.1999
M0114
1.5.8.2
0.32190.13840.11990.237910.28150.07490.38560.1499
M0006
1.8.1.7
0.23780.20980.180.38350.281510.16500.11990.0895
M0123
1.8.99.2
0.2250.26460.30450.06210.07490.165010.06300.1499
M0131
1.14.13.2
0.30980.10580.09460.25830.38560.11990.063010.1038
M0142
1.18.1.2
0.11250.14110.11940.19990.14990.08950.14990.10381

Cofactors

Number of Metal Cofactors Number of Organic CofactorsFADFMNFe(III)4S4Fe(III)4S42Fe2S2Fe3S4Fe4S4GlutathioneHeme C
M0108
1.3.1.34
1 2 111
M0294
1.3.5.1
3 1 1111
M0020
1.3.99.1
4 1 14
M0113
1.5.3.1
1 1
M0114
1.5.8.2
1 1 11
M0006
1.8.1.7
2 11
M0123
1.8.99.2
2 1 12
M0131
1.14.13.2
1 1
M0142
1.18.1.2
1 1

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
1 to 2
C-C
2 to 1
C-H
Formed
C-H
Cleaved
C-N
Cleaved
C-N
1 to 2
C-O
Formed
C-O
Formed
C-O
1 to 2
N-H
Formed
N-H
Cleaved
O-H
Formed
O-H
Cleaved
O-O
Cleaved
O-O
2 to 1
S-H
Formed
S-O
Cleaved
S-O
2 to 1
S-S
Cleaved
M0108
1.3.1.34
12211
M0294
1.3.5.1
12111
M0020
1.3.99.1
12
M0113
1.5.3.1
1111221
M0114
1.5.8.2
11112
M0006
1.8.1.7
111121
M0123
1.8.99.2
111
M0131
1.14.13.2
11211311
M0142
1.18.1.2
1111

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

M0108
1.3.1.34
M0294
1.3.5.1
M0020
1.3.99.1
M0113
1.5.3.1
M0114
1.5.8.2
M0006
1.8.1.7
M0123
1.8.99.2
M0131
1.14.13.2
M0142
1.18.1.2
M0108
1.3.1.34
10.58330.60.04340.05550.333300.250.5
M0294
1.3.5.1
0.583310.625000.133300.080.2
M0020
1.3.99.1
0.60.6251000.076900.04340.125
M0113
1.5.3.1
0.04340010.61530.04760.14280.45450.0625
M0114
1.5.8.2
0.0555000.615310.062500.17390.0909
M0006
1.8.1.7
0.33330.13330.07690.04760.0625100.21730.4444
M0123
1.8.99.2
0000.14280010.15780
M0131
1.14.13.2
0.250.080.04340.45450.17390.21730.157810.2777
M0142
1.18.1.2
0.50.20.1250.06250.09090.444400.27771

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
M0108
1.3.1.34
7 6 36 6 6 6 24
M0294
1.3.5.1
6 3 25 8.33 6 7 10
M0020
1.3.99.1
3 3 29 9.66 8 8 13
M0113
1.5.3.1
9 6 34 5.66 13 13 8
M0114
1.5.8.2
6 4 16 4 4 5 7
M0006
1.8.1.7
7 6 30 5 8 9 13
M0123
1.8.99.2
3 5 18 3.6 4 5 9
M0131
1.14.13.2
11 9 96 10.66 36 36 24
M0142
1.18.1.2
4 3 13 4.33 2 2 9

C-C
Cleaved
C-C
Stereo
C-C
1 to 2
C-C
2 to 1
C-H
Formed
C-H
Cleaved
C-N
Formed
C-N
Cleaved
C-N
1 to 2
C-N
Cleaved
C-N
2 to 1
C-N
Stereo
C-O
Formed
C-O
Formed
C-O
Cleaved
C-O
1 to 2
C-O
2 to 1
C-S
Formed
C-S
Cleaved
N-H
Formed
N-H
Cleaved
N-S
Formed
N-S
Cleaved
O-H
Formed
O-H
Cleaved
O-O
Cleaved
O-O
2 to 1
R-H
Formed
R-H
Cleaved
S-H
Formed
S-H
Cleaved
S-O
Cleaved
S-O
1 to 2
S-O
2 to 1
S-S
Formed
S-S
Cleaved
M0108
1.3.1.34
672154112223
M0294
1.3.5.1
11232121222321
M0020
1.3.99.1
232222244231
M0113
1.5.3.1
1111131211142671
M0114
1.5.8.2
11131212112
M0006
1.8.1.7
2214311112213123
M0123
1.8.99.2
1122111122112
M0131
1.14.13.2
33287211166282611
M0142
1.18.1.2
22132111

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.


M0108
1.3.1.34
M0294
1.3.5.1
M0020
1.3.99.1
M0113
1.5.3.1
M0114
1.5.8.2
M0006
1.8.1.7
M0123
1.8.99.2
M0131
1.14.13.2
M0142
1.18.1.2
M0108
1.3.1.34
10.31960.64650.39350.380.32810.33980.16940.33
M0294
1.3.5.1
0.319610.43820.29660.36360.40780.250.0530.4285
M0020
1.3.99.1
0.64650.438210.4640.45830.39790.34610.15480.3333
M0113
1.5.3.1
0.39350.29660.46410.36840.22720.31310.25120.1682
M0114
1.5.8.2
0.380.36360.45830.368410.42370.40540.08470.6785
M0006
1.8.1.7
0.32810.40780.39790.22720.423710.21730.05490.4107
M0123
1.8.99.2
0.33980.250.34610.31310.40540.217310.0880.3823
M0131
1.14.13.2
0.16940.0530.15480.25120.08470.05490.08810.0396
M0142
1.18.1.2
0.330.42850.33330.16820.67850.41070.38230.03961

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.


M0108
1.3.1.34
M0294
1.3.5.1
M0020
1.3.99.1
M0113
1.5.3.1
M0114
1.5.8.2
M0006
1.8.1.7
M0123
1.8.99.2
M0131
1.14.13.2
M0142
1.18.1.2
M0108
1.3.1.34
10.39070.58400.28050.33300.30600.27710.21250.2926
M0294
1.3.5.1
0.390710.51960.21920.27090.33080.22860.06890.3338
M0020
1.3.99.1
0.58400.519610.32520.32780.31130.30100.12860.2589
M0113
1.5.3.1
0.28050.21920.325210.36040.24830.23330.27330.1655
M0114
1.5.8.2
0.33300.27090.32780.360410.35200.28220.16880.4875
M0006
1.8.1.7
0.30600.33080.31130.24830.352010.18240.08730.3337
M0123
1.8.99.2
0.27710.22860.30100.23330.28220.182410.08870.2859
M0131
1.14.13.2
0.21250.06890.12860.27330.16880.08730.088710.0794
M0142
1.18.1.2
0.29260.33380.25890.16550.48750.33370.28590.07941
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