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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 M0234 and M0197

These two reactions have a combined similarity of 0.24


M0234

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Comparison

M0197

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EC 6.3.5.2
GMP synthase (glutamine-hydrolysing)
Sub-Class EC 6.1.1.1
tyrosine-tRNA ligase

Image of xanthosine 5'-phosphate

Image of L-glutamine

Image of ATP

Image of Water

right arrow

Image of L-glutamic acid

Image of AMP

Image of GMP

Image of diphosphate

xanthosine 5'-phosphate
C00655
CHEBI:53012
L-glutamine
C00064
CHEBI:32666
ATP
C00002
CHEBI:30616
Water
C00001
CHEBI:15377
L-glutamic acid
C00025
CHEBI:16015
AMP
C00020
CHEBI:456215
GMP
C00144
CHEBI:58115
diphosphate
C00013
CHEBI:33019
0.66

Image of L-tyrosine

Image of ATP

Image of tRNA(Tyr)

right arrow

Image of L-tyrosyl-tRNA(Tyr)

Image of AMP

Image of diphosphate

L-tyrosine
C00082
CHEBI:58315
ATP
C00002
CHEBI:30616
tRNA(Tyr)
C00787
CHEBI:29182
L-tyrosyl-tRNA(Tyr)
C02839
CHEBI:29161
AMP
C00020
CHEBI:456215
diphosphate
C00013
CHEBI:33019

Catalytic CATH Codes

3.40.50.880
3.40.50.620

Catalytic CATH Codes

3.40.50.620
1.10.240.10

Active Site



0.25713

Active Site



Catalytic Residues

Type Number Chain Location of Function
Lys 381 B Side Chain
Asp 239 B Side Chain
Glu 183 B Side Chain
His 181 B Side Chain
Cys 86 B Side Chain
Gly 59 B Main Chain Amide
Tyr 87 B Main Chain Amide
0.2857

Catalytic Residues

Type Number Chain Location of Function
Thr 40 A Side Chain
His 45 A Side Chain
His 48 A Side Chain
Lys 82 A Side Chain
Arg 86 A Side Chain
Gln 173 A Side Chain
Lys 230 A Side Chain
Lys 233 A Side Chain
Thr 234 A Side Chain
Asp 194 A Side Chain

Organic Cofactors

No Associated Organic Cofactors

Organic Cofactors

No Associated Organic Cofactors

Metal Cofactors

Type Het group Number Chain
magnesium MG 530 B

Metal Cofactors

Type Het group Number Chain
magnesium MG(not in PDB) 1 x

Reaction occurs across 6 steps

0.1707

Reaction occurs across 2 steps

Step 1
GIF of Reaction Step M0234.stg01

The beta-phosphate deprotonates the XMP substrate, which then initiates a nucleophilic attack on the alpha-phosphate of ATP, eliminating pyrophosphate.
0.5 Step 1
GIF of Reaction Step M0197.stg01

The carboxylate group of the substrate L-tyrosine acts as a nucleophile and attacks the alpha-phosphate of the ATP in a substitution reaction that liberates pyrophosphate. Mg(II) and all catalytic residues stabilise the intermediates formed. Thr234 also affects the steric outcome of the reaction.
Step 2
GIF of Reaction Step M0234.stg02

His181 deprotonates Cys86, activating it for a nucleophilic attack upon L-glutamine, forming an enzyme-substrate covalent bond.
0 Step 2
GIF of Reaction Step M0197.stg02

The phosphate of the tyrosine-AMP complex deprotonates the OH of the ribose ring, which acts as a nucleophile to attack the carbonyl group of the tyrosine in the tyrosine-AMP complex in a substitution reaction, liberating AMP. Mg(II), Thr40, His48, Lys82, Arg86 and Gln173 all stabilise the intermediates formed.
Step 3
GIF of Reaction Step M0234.stg03

The tetrahedral intermediate collapses, liberating ammonia, which deprotonates His181 and then passes to the other catalytic domain.
N/A Step 3
No Step with this number present
Step 4
GIF of Reaction Step M0234.stg04

Ammonia is deprotonated by the phosphate of the intermediate, activating it for a nucleophilic attack on the intermediate, which liberates AMP and the GMP product.
N/A Step 4
No Step with this number present
Step 5
GIF of Reaction Step M0234.stg05

His181 deprotonates a water molecule, which initiates a nucleophilic attack on the Cys-bound intermediate.
N/A Step 5
No Step with this number present
Step 6
GIF of Reaction Step M0234.stg06

The tetrahedral intermediate collapses, liberating Cys86, which deprotonates His181, and the glutamate product.
N/A Step 6
No Step with this number present

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