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Analysis of the D-Amino Acid Oxidase, subunit A, domain 2 (CATH:3.30.9.10) dataset

There are 3 entries in this dataset.


Entry Number Enzyme Name EC Code PDB Code CATH Code
M0110
Structure Overview
D-amino-acid oxidase 1.4.3.3 1c0p 3.40.50.720
3.30.9.10
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
M0131
Structure Overview
4-hydroxybenzoate 3-monooxygenase 1.14.13.2 1doc 3.50.50.60
3.30.9.10

EC Class Composition

    


CATH Domain Composition

Step Analysis

There are an average of 6.66 number of steps in this dataset. The median number of steps is 9. The maximum number of steps in this dataset is 9 and the minimum is 5. 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 4.33 number of catalytic amino acid residues in a MACiE reaction for this dataset. The maximum number of amino acid residues in this dataset is 5 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 D-Amino Acid Oxidase, subunit A, domain 2 (CATH:3.30.9.10) Entries

Activation Steric Stabilisation Proton Shuttling Hydrogen Shuttling Single Electron Shuttling Electron Pair Shuttling Covalent Catalysis
Arg--------
Asn--------
Asp--------
Cys
(0.33)
1
0.33
-------
Gln--------
Glu--------
His
(0.66)
---1
0.66
----
Lys
(0.66)
-0.33
0.22
0.66
0.44
0.33
0.22
----
Phe--------
Ser
(0.33)
---1
0.33
----
Thr
(0.33)
---1
0.33
----
Trp--------
Tyr
(0.33)
---1
0.33
----

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.


M0110
1.4.3.3
M0113
1.5.3.1
M0131
1.14.13.2
M0110
1.4.3.3
100
M0113
1.5.3.1
010.2583
M0131
1.14.13.2
00.25831

Cofactors

Number of Metal Cofactors Number of Organic CofactorsFAD
M0110
1.4.3.3
1 1
M0113
1.5.3.1
1 1
M0131
1.14.13.2
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
Cleaved
C-N
Cleaved
C-N
1 to 2
C-O
Formed
C-O
Formed
N-H
Formed
O-H
Formed
O-H
Cleaved
O-O
Cleaved
O-O
2 to 1
M0110
1.4.3.3
1111221
M0113
1.5.3.1
1111221
M0131
1.14.13.2
11211311

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

M0110
1.4.3.3
M0113
1.5.3.1
M0131
1.14.13.2
M0110
1.4.3.3
110.4545
M0113
1.5.3.1
110.4545
M0131
1.14.13.2
0.45450.45451

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
M0110
1.4.3.3
9 5 26 5.2 9 9 8
M0113
1.5.3.1
9 6 34 5.66 13 13 8
M0131
1.14.13.2
11 9 96 10.66 36 36 24

C-C
1 to 2
C-C
2 to 1
C-H
Cleaved
C-N
Formed
C-N
Cleaved
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
N-H
Formed
N-H
Cleaved
O-H
Formed
O-H
Cleaved
O-O
Cleaved
O-O
2 to 1
M0110
1.4.3.3
11131211132441
M0113
1.5.3.1
1111131211142671
M0131
1.14.13.2
33287211166282611

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.


M0110
1.4.3.3
M0113
1.5.3.1
M0131
1.14.13.2
M0110
1.4.3.3
10.68750.1842
M0113
1.5.3.1
0.687510.2512
M0131
1.14.13.2
0.18420.25121

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.


M0110
1.4.3.3
M0113
1.5.3.1
M0131
1.14.13.2
M0110
1.4.3.3
10.54680.1651
M0113
1.5.3.1
0.546810.2733
M0131
1.14.13.2
0.16510.27331
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