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Analysis of the Rossmann fold (CATH:3.40.50.970) dataset

There are 9 entries in this dataset.


Entry Number Enzyme Name EC Code PDB Code CATH Code
M0274
Structure Overview
pyruvate oxidase 1.2.3.3 1pow 3.40.50.970
M0106
Structure Overview
pyruvate dehydrogenase (acetyl-transferring) 1.2.4.1 1w85 3.40.50.970
3.40.50.970
3.40.50.920
4.10.320.10
M0280
Structure Overview
3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) 1.2.4.4 1dtw 3.40.50.970
3.40.50.920
M0119
Structure Overview
pyruvate:ferredoxin oxidoreducatse 1.2.7.1 2c3m 3.40.50.970
3.30.70.20
4.10.790.10
4.10.780.10
3.40.50.920
3.40.50.970
3.40.920.10
M0219
Structure Overview
transketolase 2.2.1.1 1trk 3.40.50.970
3.40.50.920
3.40.50.970
M0289
Structure Overview
acetolactate synthase 2.2.1.6 1n0h 3.40.50.970
3.40.50.970
3.40.50.1220
M0215
Structure Overview
pyruvate decarboxylase 4.1.1.1 1pvd 3.40.50.970
3.40.50.1220
M0220
Structure Overview
benzoylformate decarboxylase 4.1.1.7 1mcz 3.40.50.1220
3.40.50.970
3.40.50.1220
3.40.50.970
M0221
Structure Overview
benzoin aldolase 4.1.2.38 2ag0 3.40.50.970
Unassigned

EC Class Composition

    


CATH Domain Composition

Step Analysis

There are an average of 7.22 number of steps in this dataset. The median number of steps is 7. The maximum number of steps in this dataset is 12 and the minimum is 6. 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 4.77 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 4. 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 Rossmann fold (CATH:3.40.50.970) Entries

Activation Steric Stabilisation Proton Shuttling Hydrogen Shuttling Single Electron Shuttling Electron Pair Shuttling Covalent Catalysis
Arg
(0.22)
--1
0.22
-----
Asn
(0.11)
--1
0.11
-----
Asp
(0.11)
---1
0.11
----
Cys--------
Gln
(0.33)
0.33
0.11
-0.66
0.22
-----
Glu
(1)
0.18
0.18
0.09
0.09
0.18
0.18
0.81
0.81
----
His
(0.66)
0.27
0.18
0.09
0.06
0.36
0.24
0.72
0.48
----
Lys
(0.11)
--------
Phe
(0.11)
1
0.11
-1
0.11
-----
Ser
(0.22)
--0.5
0.11
-----
Thr
(0.11)
--1
0.11
-----
Trp--------
Tyr
(0.11)
--1
0.11
-----

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.


M0274
1.2.3.3
M0106
1.2.4.1
M0280
1.2.4.4
M0119
1.2.7.1
M0219
2.2.1.1
M0289
2.2.1.6
M0215
4.1.1.1
M0220
4.1.1.7
M0221
4.1.2.38
M0274
1.2.3.3
10.07520.07760.08710.07060.21220.12650.12230.1882
M0106
1.2.4.1
0.075210.27650.20340.64880.10680.49080.49080.3543
M0280
1.2.4.4
0.07760.276510.10370.29990.09990.29990.5510.234
M0119
1.2.7.1
0.08710.20340.103710.08090.12850.16190.15540.1457
M0219
2.2.1.1
0.07060.64880.29990.080910.06920.61090.61780.36
M0289
2.2.1.6
0.21220.10680.09990.12850.069210.16370.15980.3199
M0215
4.1.1.1
0.12650.49080.29990.16190.61090.163710.73620.5353
M0220
4.1.1.7
0.12230.49080.5510.15540.61780.15980.736210.5260
M0221
4.1.2.38
0.18820.35430.2340.14570.360.31990.53530.52601

Cofactors

Number of Metal Cofactors Number of Organic CofactorsCa(II)FADFe(III)4S42K(I)Mg(II)Thiamine diphosphate
M0274
1.2.3.3
1 2 111
M0106
1.2.4.1
1 1 11
M0280
1.2.4.4
2 1 111
M0119
1.2.7.1
4 1 311
M0219
2.2.1.1
1 1 11
M0289
2.2.1.6
1 1 11
M0215
4.1.1.1
1 1 11
M0220
4.1.1.7
1 1 11
M0221
4.1.2.38
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-H
Formed
C-H
Stereo
C-O
Formed
C-O
Stereo
C-O
1 to 2
C-O
2 to 1
C-S
Formed
O-H
Formed
O-H
Cleaved
O-O
2 to 1
S-H
Formed
S-H
Cleaved
S-S
Cleaved
M0274
1.2.3.3
111211
M0106
1.2.4.1
11111
M0280
1.2.4.4
111111
M0119
1.2.7.1
1111
M0219
2.2.1.1
11111111
M0289
2.2.1.6
1111
M0215
4.1.1.1
1111
M0220
4.1.1.7
1111
M0221
4.1.2.38
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

M0274
1.2.3.3
M0106
1.2.4.1
M0280
1.2.4.4
M0119
1.2.7.1
M0219
2.2.1.1
M0289
2.2.1.6
M0215
4.1.1.1
M0220
4.1.1.7
M0221
4.1.2.38
M0274
1.2.3.3
10.16660.250.18180.41660.44440.30.30.3
M0106
1.2.4.1
0.166610.83330.50.08330.28570.28570.28570.2857
M0280
1.2.4.4
0.250.833310.42850.16660.250.42850.42850.4285
M0119
1.2.7.1
0.18180.50.428510.09090.33330.33330.33330.3333
M0219
2.2.1.1
0.41660.08330.16660.090910.33330.20.20.2
M0289
2.2.1.6
0.44440.28570.250.33330.333310.33330.33330.3333
M0215
4.1.1.1
0.30.28570.42850.33330.20.3333111
M0220
4.1.1.7
0.30.28570.42850.33330.20.3333111
M0221
4.1.2.38
0.30.28570.42850.33330.20.3333111

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
M0274
1.2.3.3
7 12 49 4.08 11 11 27
M0106
1.2.4.1
5 8 32 4 10 11 11
M0280
1.2.4.4
6 7 32 4.57 10 11 11
M0119
1.2.7.1
4 7 29 4.14 8 8 13
M0219
2.2.1.1
8 7 52 7.42 14 13 25
M0289
2.2.1.6
4 6 26 4.33 8 6 12
M0215
4.1.1.1
4 6 50 8.33 12 13 25
M0220
4.1.1.7
4 6 34 5.66 9 10 15
M0221
4.1.2.38
4 6 36 6 10 11 15

C-C
Formed
C-C
Cleaved
C-C
1 to 2
C-C
2 to 1
C-H
Formed
C-H
Cleaved
C-N
1 to 2
C-N
2 to 1
C-O
Formed
C-O
1 to 2
C-O
2 to 1
C-S
Formed
N-H
Formed
N-H
Cleaved
O-H
Formed
O-H
Cleaved
O-O
2 to 1
S-H
Formed
S-H
Cleaved
S-S
Cleaved
M0274
1.2.3.3
1244226514333441
M0106
1.2.4.1
12221122211442311
M0280
1.2.4.4
12221122211442311
M0119
1.2.7.1
1222113321122321
M0219
2.2.1.1
225511551235555
M0289
2.2.1.6
21221122222232
M0215
4.1.1.1
12552155325545
M0220
4.1.1.7
12332133214423
M0221
4.1.2.38
12332133214434

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.


M0274
1.2.3.3
M0106
1.2.4.1
M0280
1.2.4.4
M0119
1.2.7.1
M0219
2.2.1.1
M0289
2.2.1.6
M0215
4.1.1.1
M0220
4.1.1.7
M0221
4.1.2.38
M0274
1.2.3.3
10.59250.59250.6470.8820.57850.90110.74610.7835
M0106
1.2.4.1
0.5925110.76560.61530.74190.64860.89470.8795
M0280
1.2.4.4
0.5925110.76560.61530.74190.64860.89470.8795
M0119
1.2.7.1
0.6470.76560.765610.56370.85410.58450.78570.7792
M0219
2.2.1.1
0.8820.61530.61530.563710.53020.96750.74830.8039
M0289
2.2.1.6
0.57850.74190.74190.85410.530210.52770.73910.7368
M0215
4.1.1.1
0.90110.64860.64860.58450.96750.527710.80280.8482
M0220
4.1.1.7
0.74610.89470.89470.78570.74830.73910.802810.9764
M0221
4.1.2.38
0.78350.87950.87950.77920.80390.73680.84820.97641

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.


M0274
1.2.3.3
M0106
1.2.4.1
M0280
1.2.4.4
M0119
1.2.7.1
M0219
2.2.1.1
M0289
2.2.1.6
M0215
4.1.1.1
M0220
4.1.1.7
M0221
4.1.2.38
M0274
1.2.3.3
10.42050.42950.46050.63260.47350.64730.54550.5863
M0106
1.2.4.1
0.420510.80240.59840.57040.53750.57280.73280.6888
M0280
1.2.4.4
0.42950.802410.56640.49150.53220.53940.76210.6730
M0119
1.2.7.1
0.46050.59840.566410.39570.62060.45370.58280.5762
M0219
2.2.1.1
0.63260.57040.49150.395710.39520.80160.66080.6325
M0289
2.2.1.6
0.47350.53750.53220.62060.395210.41720.55360.5922
M0215
4.1.1.1
0.64730.57280.53940.45370.80160.417210.80580.7851
M0220
4.1.1.7
0.54550.73280.76210.58280.66080.55360.805810.8661
M0221
4.1.2.38
0.58630.68880.67300.57620.63250.59220.78510.86611
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