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The two reactions compared are done so using a Tanimoto similarity score (for more information, please see the MACiE FAQ) for the bond changes only. The score maay range from 0 to 1 where 1 indicates that the two reactions are identical at the bond change level and 0 indicates that there are no bond changes in common.


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

Results for Comparison of M0074 and M0212

These two reactions have a combined similarity of 0.12


M0074

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Comparison

M0212

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EC 6.3.3.3
dethiobiotin synthase
Class EC 1.18.6.1
nitrogenase

Image of ATP

Image of carbon dioxide

Image of 7,8-diaminononanoate

right arrow

Image of proton

Image of dethiobiotin

Image of ADP

Image of phosphate

ATP
C00002
CHEBI:30616
carbon dioxide
C00011
CHEBI:16526
7,8-diaminononanoate
C01037
CHEBI:17830
proton
C00080
CHEBI:24636
dethiobiotin
C01909
CHEBI:57861
ADP
C00008
CHEBI:456216
phosphate
C00009
CHEBI:39745
0.06

Image of proton

Image of ATP

Image of nitrogen

Image of reduced ferredoxin

Image of water

right arrow

Image of proton

Image of oxidised ferredoxin

Image of dihydrogen

Image of phosphate

Image of ammonia

Image of ADP

8 proton
C00008
CHEBI:24636
8 ATP
C00002
CHEBI:30616
nitrogen
C00697
CHEBI:17997
8 reduced ferredoxin
C00138
CHEBI:17513
8 water
C00001
CHEBI:15377
8 proton
C00080
CHEBI:24636
8 oxidised ferredoxin
C00139
CHEBI:17908
dihydrogen
C00282
CHEBI:18276
8 phosphate
C00009
CHEBI:18367
2 ammonia
C00014
CHEBI:16134
8 ADP
C00008
CHEBI:456216

Catalytic CATH Codes

3.40.50.300

Catalytic CATH Codes

3.40.50.1980
3.40.50.300

Active Site



0.31761

Active Site



Catalytic Residues

Type Number Chain Location of Function
Lys 15 A Side Chain
Lys 37 A Side Chain
Ser 41 A Main Chain Amide
0.3529

Catalytic Residues

Type Number Chain Location of Function
Val 157 B Main Chain
Lys 15 F Side Chain
Lys 41 F Side Chain
Lys 10 E Side Chain
Asp 129 E Side Chain
Cys 153 B Side Chain
Cys 62 A Side Chain
His 195 A Side Chain
Arg 96 A Side Chain
Ala 65 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
magnesium MG 901 x
magnesium MG 902 x

Metal Cofactors

Type Het group Number Chain
magnesium MG 292 E
iron CFM 496 A
molybdenum CFM 496 A
iron CLF 498 A
iron SF4 290 E

Reaction occurs across 4 steps

0.0623

Reaction occurs across 15 steps

Step 1
GIF of Reaction Step M0074.stg01

Water deprotonates the 7,8-diaminononanoate substrate, activating it for a nucleophilic attack upon the carbon dioxide in an addition reaction. Lys37 stabilises the formation of the negatively charged intermediate.
0.11 Step 1
GIF of Reaction Step M0212.stg01

Asp129E deprotonates water, which initiates an electrophilic substitution at the gamma-phosphate of ATP, producing phosphate and ADP. This initiates a single electron transfer from the iron-sulfur cluster, through Val157B Cys153B, the P-cluster, Ala65A to the Fe-Mo-S cluster cofactor, one of the sulfurs (S3B) in this cofactor then deprotonates water.
Step 2
GIF of Reaction Step M0074.stg02

The carboxylated intermediate acts as a nucleophile and attacks the gamma phosphate of ATP in a substitution reaction. Lys37, Lys15 and two Mg(II) ions stabilise the intermediates.
0 Step 2
GIF of Reaction Step M0212.stg02

A new molecule of ATP displaces the product ADP. Ferredoxin transfers a single electron back to the iron-sulfur cluster
Step 3
GIF of Reaction Step M0074.stg03

The newly attached phosphate group deprotonates the terminal primary amine, which in turn acts as a nucleophile to attack the phosphorylated carbonyl carbon in an internal addition reaction. Lys37, Lys15 and the main chain amide of Ser41 all stabilise the intermediates.
0.1 Step 3
GIF of Reaction Step M0212.stg03

The proton on the S3B is transferred to a different atom in the cofactor and a second proton is transferred via the water chain.
Step 4
GIF of Reaction Step M0074.stg04

The oxyanion formed re-forms the carbonyl group, cleaving the P-O bond in a conjugate base elimination reaction. The leaving phosphate group deprotonates the newly formed secondary amine. Lys15, Lys37 and the main chain amide of Ser41 all stabilise the intermediates.
0 Step 4
GIF of Reaction Step M0212.stg04

Dihydrogen is eliminated from the Fe-Mo-S cluster cofactor
Step 5
No Step with this number present
N/A Step 5
GIF of Reaction Step M0212.stg05

A further two protons are transferred from the bulk solvent to the FeMo-cofactor. Dinitrogen is then bound to one of the iron atoms in the Fe-Mo-S cluster cofactor in a nucleophilic addition.
Step 6
No Step with this number present
N/A Step 6
GIF of Reaction Step M0212.stg06

Dinitrogen is bound in a bidentate manner through an electrophilic addition.
Step 7
No Step with this number present
N/A Step 7
GIF of Reaction Step M0212.stg07

A proton is transferred to the bound dinitrogen from the S3B thiol, which reprotonates from water.
Step 8
No Step with this number present
N/A Step 8
GIF of Reaction Step M0212.stg08

A second proton is transferred to the bound dinitrogen from the S3B thiol, which reprotonates from water.
Step 9
No Step with this number present
N/A Step 9
GIF of Reaction Step M0212.stg09

In a nucleophilic substitution, the diimide becomes bound in a monodentate manner, and another proton is transferred from the S3B thiol, which reprotonates from water.
Step 10
No Step with this number present
N/A Step 10
GIF of Reaction Step M0212.stg10

The hydrazine intermediate gains another proton from the S3B thiol, which reprotonates from water.
Step 11
No Step with this number present
N/A Step 11
GIF of Reaction Step M0212.stg11

In an elimination reaction, the N-N bond is cleaved, resulting in ammonia and a further proton being transferred from the S3B thiol, which reprotonates from water.
Step 12
No Step with this number present
N/A Step 12
GIF of Reaction Step M0212.stg12

In a nucleophilic substitution reaction the cental nitrogen atom of the cofactor reforms one of its bonds to the one of the iron centres.
Step 13
No Step with this number present
N/A Step 13
GIF of Reaction Step M0212.stg13

The amine then deprotonates one of the thiol groups, resulting in a thiolate.
Step 14
No Step with this number present
N/A Step 14
GIF of Reaction Step M0212.stg14

The thiolate attacks the iron centre to which the amine group is bound in a nucleophilic substitution, producing the second ammonia.
Step 15
No Step with this number present
N/A Step 15
GIF of Reaction Step M0212.stg15

The cofactor regenerates its initial protonation state through proton transfer.

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