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Analysis of the NAD(P)-binding Rossmann-like Domain (CATH:3.40.50.720) dataset

There are 16 entries in this dataset.


Entry Number Enzyme Name EC Code PDB Code CATH Code
M0256
Structure Overview
alcohol dehydrogenase 1.1.1.1 1qlh 3.90.180.10
3.40.50.720
M0255
Structure Overview
alcohol dehydrogenase 1.1.1.1 1mg5 3.40.50.720
3.40.50.720
M0092
Structure Overview
UDP-glucose 6-dehydrogenase 1.1.1.22 1dli 3.40.50.720
1.10.1040.10
3.40.50.1870
M0021
Structure Overview
malate dehydrogenase (oxaloacetate-decarboxylating) 1.1.1.38 1do8 3.40.50.10380
3.40.50.720
M0227
Structure Overview
GDP-L-fucose synthase 1.1.1.271 1e6u 3.40.50.720
3.90.25.10
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
M0110
Structure Overview
D-amino-acid oxidase 1.4.3.3 1c0p 3.40.50.720
3.30.9.10
M0237
Structure Overview
pteridine reductase 1.5.1.33 2c7v 3.40.50.720
M0114
Structure Overview
trimethylamine dehydrogenase 1.5.8.2 2tmd 3.20.20.70
3.50.50.60
3.40.50.720
M0116
Structure Overview
NAD(P)+ transhydrogenase (AB-specific) 1.6.1.2 1hzz 3.40.50.720
3.40.50.1770
3.40.50.1220
3.40.50.720
3.40.50.1770
M0142
Structure Overview
ferredoxin-NADP+ reductase 1.18.1.2 1e6e 3.40.50.720
3.50.50.60
3.10.20.30
M0090
Structure Overview
adenosylhomocysteinase 3.3.1.1 1b3r 3.40.50.1480
3.40.50.720
M0226
Structure Overview
UDP-sulfoquinovose synthase 3.13.1.1 1qrr 3.40.50.720
3.90.25.10
M0228
Structure Overview
dTDP-glucose 4,6-dehydratase 4.2.1.46 1bxk 3.40.50.720
3.90.25.10
3.40.50.720
M0188
Structure Overview
UDP-glucose 4-epimerase 5.1.3.2 1xel 3.40.50.720
3.90.25.10
M0317
Structure Overview
UDP-N-acetylmuramoyl-L-alanine---D-glutamate ligase 6.3.2.9 1uag 3.40.1190.10
3.90.190.20
3.40.50.720

EC Class Composition

    


CATH Domain Composition

Step Analysis

There are an average of 4 number of steps in this dataset. The median number of steps is 4. 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 4.25 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 2. 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 NAD(P)-binding Rossmann-like Domain (CATH:3.40.50.720) Entries

Activation Steric Stabilisation Proton Shuttling Hydrogen Shuttling Single Electron Shuttling Electron Pair Shuttling Covalent Catalysis
Arg
(0.25)
-0.5
0.12
0.75
0.18
-----
Asn
(0.25)
-0.25
0.06
1
0.25
-----
Asp
(0.43)
-0.11
0.04
0.22
0.09
0.77
0.33
----
Cys
(0.25)
0.5
0.12
-0.5
0.12
----0.25
0.06
Gln
(0.06)
-----1
0.06
--
Glu
(0.18)
--0.33
0.06
0.66
0.12
----
His
(0.5)
0.22
0.11
0.11
0.05
0.22
0.11
0.55
0.27
----
Lys
(0.56)
0.55
0.31
-0.77
0.43
0.33
0.18
----
Phe--------
Ser
(0.43)
0.37
0.16
0.12
0.05
0.5
0.21
0.37
0.16
----
Thr
(0.18)
0.66
0.12
0.33
0.06
1
0.18
-----
Trp--------
Tyr
(0.62)
0.1
0.06
0.2
0.12
0.3
0.18
0.8
0.49
----

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.


M0256
1.1.1.1
M0255
1.1.1.1
M0092
1.1.1.22
M0021
1.1.1.38
M0227
1.1.1.271
M0108
1.3.1.34
M0110
1.4.3.3
M0237
1.5.1.33
M0114
1.5.8.2
M0116
1.6.1.2
M0142
1.18.1.2
M0090
3.3.1.1
M0226
3.13.1.1
M0228
4.2.1.46
M0188
5.1.3.2
M0317
6.3.2.9
M0256
1.1.1.1
10.22500.00840.38560.16240.23560.01270.237600.180.24540.37100.2250.2349
M0255
1.1.1.1
0.22510.11250.29990.51420.13840.180.22290.20590.1420.02090.15090.58880.358910.1957
M0092
1.1.1.22
00.112510.33750.14990.10450.13490.130.12740.180.2250.35750.19990.53040.11250.2571
M0021
1.1.1.38
0.00840.29990.337510.17410.23630.14070.54840.13650.53110.12330.28680.2360.38560.29990.3221
M0227
1.1.1.271
0.38560.51420.14990.174110.16360.19990.090.35350.08980.08180.39920.58750.21640.51420.2299
M0108
1.3.1.34
0.16240.13840.10450.23630.163610.14210.29990.32190.19990.11250.11990.24580.24250.12850.1408
M0110
1.4.3.3
0.23560.180.13490.14070.19990.1421100000.13840.144500.21440.2017
M0237
1.5.1.33
0.01270.22290.130.54840.090.2999010.180.720.17160.13840.15850.33190.22290
M0114
1.5.8.2
0.23760.20590.12740.13650.35350.321900.1810.11250.14990.23580.29990.12850.180.18
M0116
1.6.1.2
00.1420.180.53110.08980.199900.720.112510.2250.26530.090.35920.11250
M0142
1.18.1.2
0.180.02090.2250.12330.08180.112500.17160.14990.22510.31590.27260.25710.01820.1499
M0090
3.3.1.1
0.24540.15090.35750.28680.39920.11990.13840.13840.23580.26530.315910.27680.19270.15250.3432
M0226
3.13.1.1
0.3710.58880.19990.2360.58750.24580.14450.15850.29990.090.27260.276810.42310.58880.2999
M0228
4.2.1.46
00.35890.53040.38560.21640.242500.33190.12850.35920.25710.19270.423110.35490.1439
M0188
5.1.3.2
0.22510.11250.29990.51420.12850.21440.22290.180.11250.01820.15250.58880.354910.198
M0317
6.3.2.9
0.23490.19570.25710.32210.22990.14080.201700.1800.14990.34320.29990.14390.1981

Cofactors

Number of Metal Cofactors Number of Organic CofactorsFADFMNFe(III)4S4Mg(II)Mn(II)NADZn(II)
M0256
1.1.1.1
1 1 11
M0255
1.1.1.1
1 1
M0092
1.1.1.22
M0021
1.1.1.38
1 1
M0227
1.1.1.271
M0108
1.3.1.34
1 2 111
M0110
1.4.3.3
1 1
M0237
1.5.1.33
M0114
1.5.8.2
1 1 11
M0116
1.6.1.2
M0142
1.18.1.2
1 1
M0090
3.3.1.1
1 1
M0226
3.13.1.1
1 1
M0228
4.2.1.46
1 1
M0188
5.1.3.2
1 1
M0317
6.3.2.9
2 2

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
Cleaved
C-C
Stereo
C-C
1 to 2
C-C
2 to 1
C-H
Formed
C-H
Cleaved
C-H
Stereo
C-N
Formed
C-N
Cleaved
C-N
1 to 2
C-N
2 to 1
C-O
Formed
C-O
Formed
C-O
Cleaved
C-O
Stereo
C-O
1 to 2
C-O
2 to 1
C-S
Formed
C-S
Cleaved
N-H
Formed
N-H
Cleaved
O-H
Formed
O-H
Cleaved
O-O
2 to 1
P-O
Cleaved
S-H
Formed
S-O
1 to 2
M0256
1.1.1.1
1111111
M0255
1.1.1.1
1111111
M0092
1.1.1.22
22222112
M0021
1.1.1.38
11121121
M0227
1.1.1.271
1111121111
M0108
1.3.1.34
12211
M0110
1.4.3.3
1111221
M0237
1.5.1.33
2222222
M0114
1.5.8.2
11112
M0116
1.6.1.2
221111
M0142
1.18.1.2
1111
M0090
3.3.1.1
1111
M0226
3.13.1.1
11111
M0228
4.2.1.46
111111
M0188
5.1.3.2
11
M0317
6.3.2.9
11321

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

M0256
1.1.1.1
M0255
1.1.1.1
M0092
1.1.1.22
M0021
1.1.1.38
M0227
1.1.1.271
M0108
1.3.1.34
M0110
1.4.3.3
M0237
1.5.1.33
M0114
1.5.8.2
M0116
1.6.1.2
M0142
1.18.1.2
M0090
3.3.1.1
M0226
3.13.1.1
M0228
4.2.1.46
M0188
5.1.3.2
M0317
6.3.2.9
M0256
1.1.1.1
110.650.750.250.50.17640.40.250.58330.3750.10.09090.444400
M0255
1.1.1.1
110.650.750.250.50.17640.40.250.58330.3750.10.09090.444400
M0092
1.1.1.22
0.650.6510.66660.2580.480.18180.58820.21420.58330.250.11110.06890.2800
M0021
1.1.1.38
0.750.750.666610.22720.47050.1250.40.15780.44440.20.05880.05550.428500
M0227
1.1.1.271
0.250.250.2580.227210.41170.13040.32250.050.38880.307600.05880.18750.250.074
M0108
1.3.1.34
0.50.50.480.47050.411710.04340.560.05550.76920.5000.214200
M0110
1.4.3.3
0.17640.17640.18180.1250.13040.043410.10810.61530.04160.06250.13330.28570.357100.2083
M0237
1.5.1.33
0.40.40.58820.40.32250.560.108110.1250.66660.3333000.133300.0476
M0114
1.5.8.2
0.250.250.21420.15780.050.05550.61530.12510.05260.09090.20.18180.272700.0434
M0116
1.6.1.2
0.58330.58330.58330.44440.38880.76920.04160.66660.052610.6000.12500
M0142
1.18.1.2
0.3750.3750.250.20.30760.50.06250.33330.09090.61000.111100
M0090
3.3.1.1
0.10.10.11110.0588000.133300.20010.1250.111100
M0226
3.13.1.1
0.09090.09090.06890.05550.058800.285700.1818000.12510.37500.1052
M0228
4.2.1.46
0.44440.44440.280.42850.18750.21420.35710.13330.27270.1250.11110.11110.375100.1
M0188
5.1.3.2
00000.2500000000010
M0317
6.3.2.9
00000.07400.20830.04760.04340000.10520.101

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
M0256
1.1.1.1
7 1 16 16 5 5 6
M0255
1.1.1.1
7 1 14 14 5 5 4
M0092
1.1.1.22
14 6 30 5 10 9 11
M0021
1.1.1.38
10 4 22 5.5 6 7 9
M0227
1.1.1.271
11 6 36 6 12 12 12
M0108
1.3.1.34
7 6 36 6 6 6 24
M0110
1.4.3.3
9 5 26 5.2 9 9 8
M0237
1.5.1.33
14 3 30 10 8 8 14
M0114
1.5.8.2
6 4 16 4 4 5 7
M0116
1.6.1.2
8 3 10 3.33 2 2 6
M0142
1.18.1.2
4 3 13 4.33 2 2 9
M0090
3.3.1.1
4 7 32 4.57 11 11 10
M0226
3.13.1.1
5 4 29 7.25 9 9 11
M0228
4.2.1.46
6 4 26 6.5 8 9 9
M0188
5.1.3.2
2 2 16 8 4 4 8
M0317
6.3.2.9
8 5 12 2.4 5 5 2

C-C
Cleaved
C-C
1 to 2
C-C
2 to 1
C-H
Formed
C-H
Cleaved
C-N
Formed
C-N
1 to 2
C-N
Cleaved
C-N
2 to 1
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
O-H
Formed
O-H
Cleaved
O-O
2 to 1
P-O
Formed
P-O
Cleaved
S-H
Formed
S-O
1 to 2
M0256
1.1.1.1
11111211133
M0255
1.1.1.1
1111111133
M0092
1.1.1.22
22222132111155
M0021
1.1.1.38
122211312223
M0227
1.1.1.271
33331232277
M0108
1.3.1.34
672154112223
M0110
1.4.3.3
11131211132441
M0237
1.5.1.33
22223322246
M0114
1.5.8.2
11131212112
M0116
1.6.1.2
22111111
M0142
1.18.1.2
22132111
M0090
3.3.1.1
333311111133341
M0226
3.13.1.1
333311111111441
M0228
4.2.1.46
3333111155
M0188
5.1.3.2
2222111122
M0317
6.3.2.9
111113211

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.


M0256
1.1.1.1
M0255
1.1.1.1
M0092
1.1.1.22
M0021
1.1.1.38
M0227
1.1.1.271
M0108
1.3.1.34
M0110
1.4.3.3
M0237
1.5.1.33
M0114
1.5.8.2
M0116
1.6.1.2
M0142
1.18.1.2
M0090
3.3.1.1
M0226
3.13.1.1
M0228
4.2.1.46
M0188
5.1.3.2
M0317
6.3.2.9
M0256
1.1.1.1
10.9310.4920.550.2330.17350.49150.56660.40.17940.2750.41170.39060.36980.51510.0869
M0255
1.1.1.1
0.93110.50.56750.24030.150.42370.55170.30.20.20510.41530.39340.37140.53330.0952
M0092
1.1.1.22
0.4920.510.68420.67790.3750.5250.77770.28570.29030.16430.68830.73230.71790.52720.2
M0021
1.1.1.38
0.550.56750.684210.4690.37140.50.60.41460.33330.29260.6610.59640.50.57570.3333
M0227
1.1.1.271
0.2330.24030.67790.46910.53750.48830.60970.26980.250.14810.65280.67820.71420.32750.2125
M0108
1.3.1.34
0.17350.150.3750.37140.537510.41660.46660.380.36170.330.53440.50.4560.30690.1478
M0110
1.4.3.3
0.49150.42370.5250.50.48830.416610.62660.680.23330.33890.56960.51940.50580.34480.2187
M0237
1.5.1.33
0.56660.55170.77770.60.60970.46660.626610.40620.35590.23180.66660.70830.69620.55550.1506
M0114
1.5.8.2
0.40.30.28570.41460.26980.380.680.406210.23520.67850.39390.34920.29720.35290.2777
M0116
1.6.1.2
0.17940.20.29030.33330.250.36170.23330.35590.235210.12120.36660.4150.3870.50
M0142
1.18.1.2
0.2750.20510.16430.29260.14810.330.33890.23180.67850.121210.26080.23070.18180.32250.2812
M0090
3.3.1.1
0.41170.41530.68830.6610.65280.53440.56960.66660.39390.36660.260810.81150.70.53570.2463
M0226
3.13.1.1
0.39060.39340.73230.59640.67820.50.51940.70830.34920.4150.23070.811510.8970.64580.1969
M0228
4.2.1.46
0.36980.37140.71790.50.71420.4560.50580.69620.29720.3870.18180.70.89710.57890.125
M0188
5.1.3.2
0.51510.53330.52720.57570.32750.30690.34480.55550.35290.50.32250.53570.64580.578910.1111
M0317
6.3.2.9
0.08690.09520.20.33330.21250.14780.21870.15060.277700.28120.24630.19690.1250.11111

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.


M0256
1.1.1.1
M0255
1.1.1.1
M0092
1.1.1.22
M0021
1.1.1.38
M0227
1.1.1.271
M0108
1.3.1.34
M0110
1.4.3.3
M0237
1.5.1.33
M0114
1.5.8.2
M0116
1.6.1.2
M0142
1.18.1.2
M0090
3.3.1.1
M0226
3.13.1.1
M0228
4.2.1.46
M0188
5.1.3.2
M0317
6.3.2.9
M0256
1.1.1.1
10.76140.38480.43460.27280.20330.39600.41140.34440.17490.26120.33890.35570.28480.39100.1152
M0255
1.1.1.1
0.761410.41810.51880.30970.18210.33800.45430.27140.22380.17600.31760.4120.37550.59660.1108
M0092
1.1.1.22
0.38480.418110.59570.50390.31780.39310.59680.23890.29200.18800.54780.53280.62720.37080.1942
M0021
1.1.1.38
0.43460.51880.595710.37100.34750.37260.56710.31930.39380.24100.50720.45220.46420.44910.2971
M0227
1.1.1.271
0.27280.30970.50390.371010.43140.38040.45100.26870.22380.14740.52410.59350.53700.36640.203
M0108
1.3.1.34
0.20330.18210.31780.34750.431410.31060.43420.33300.3620.29260.37730.38640.37840.23160.1312
M0110
1.4.3.3
0.39600.33800.39310.37260.38040.310610.41810.50350.15580.22650.41810.40230.36440.27770.2134
M0237
1.5.1.33
0.41140.45430.59680.56710.45100.43420.418110.32150.47790.22690.46780.50000.54880.41680.1026
M0114
1.5.8.2
0.34440.27140.23890.31930.26870.33300.50350.321510.18620.48750.33490.32010.25250.27430.2298
M0116
1.6.1.2
0.17490.22380.29200.39380.22380.3620.15580.47790.186210.19500.30460.29220.35380.35310
M0142
1.18.1.2
0.26120.17600.18800.24100.14740.29260.22650.22690.48750.195010.24840.21810.19350.21410.2202
M0090
3.3.1.1
0.33890.31760.54780.50720.52410.37730.41810.46780.33490.30460.248410.60910.51420.38630.2458
M0226
3.13.1.1
0.35570.4120.53280.45220.59350.38640.40230.50000.32010.29220.21810.609110.72630.56690.2134
M0228
4.2.1.46
0.28480.37550.62720.46420.53700.37840.36440.54880.25250.35380.19350.51420.726310.46500.1272
M0188
5.1.3.2
0.39100.59660.37080.44910.36640.23160.27770.41680.27430.35310.21410.38630.56690.465010.1217
M0317
6.3.2.9
0.11520.11080.19420.29710.2030.13120.21340.10260.229800.22020.24580.21340.12720.12171
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