Information on EC 4.1.3.44 - tRNA 4-demethylwyosine synthase (AdoMet-dependent)

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The expected taxonomic range for this enzyme is: Archaea, Eukaryota

EC NUMBER
COMMENTARY hide
4.1.3.44
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RECOMMENDED NAME
GeneOntology No.
tRNA 4-demethylwyosine synthase (AdoMet-dependent)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
N1-methylguanine37 in tRNAPhe + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine37 in tRNAPhe + L-methionine + 5'-deoxyadenosine + CO2 + H2O
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
7-(3-amino-3-carboxypropyl)-wyosine biosynthesis
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methylwyosine biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
tRNAPhe N1-methylguanine,pyruvate acetaldehyde-lyase (tRNAPhe 4-demethylwyosine-forming, decarboxylating, dehydrating)
This enzyme, which is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes, binds two [4Fe-4S] clusters [3,4]. Carbons C2 and C3 from pyruvate are incorporated into 4-demethylwyosine [3]. The enzyme is found in eukaryotes where it is part of the pathway for wybutosine synthesis, and in archaea, where it is involved in the biosynthesis of archaeal wye bases, such as wyosine, isowyosine, and methylwyosine.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
N1-methylguanine37 in tRNAPhe + pyruvate + S-adenosyl-L-methionine
4-demethylwyosine37 in tRNAPhe + L-methionine + 5'-deoxyadenosine + CO2 + H2O
show the reaction diagram
additional information
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
N1-methylguanine37 in tRNAPhe + pyruvate + S-adenosyl-L-methionine
4-demethylwyosine37 in tRNAPhe + L-methionine + 5'-deoxyadenosine + CO2 + H2O
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Fe-S center
residues Cys81, Cys85 and Cys88 are predicted to comprise the iron-sulfur cluster. In the crystal structure, their side chains face each other to create the cluster site
[4Fe-4S]-center
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
protein contains contained up to 8.2 iron and 8.2 sulfide ions per polypeptide chain
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37000
x * 37800, calculated, x * 37000, SDS-PAGE
37800
x * 37800, calculated, x * 37000, SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 37800, calculated, x * 37000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
to 2.4 A resolution. Enzyme TYW1 assumes an incomplete TIM barrel with (alpha/beta)6 topology, which closely resembles the reported structures of radical SAM enzymes. TYW1 is considered to catalyze the cyclization reaction by utilizing the radical intermediate. construction of a model structure complexed with S-adenosylmethionine and two [4Fe-4S] clusters
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to 2.2 A resolution. The overall structure is a half-barrel structure, composed of six alpha-helices packed against a ten-stranded beta-sheet. Other alpha-helices and two long loops form the walls on both sides of the half-barrel. Construction of a docking model with the FeS clusters, AdoMet and the tRNA
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purification and reconstitution of recombinant protein
purified anaerobically and reconstituted with Fe and S. The reconstituted protein is brown and has an absorbance spectrum that displays a characteristic shoulder at 400 nm
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C444S
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loss of activity
C457S
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loss of activity
C470S
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loss of activity
C479A
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mutation in the conserved C479xxxC483xxC486 motif of the radical-Ado-Met domain, complete loss of activity
C479S
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loss of activity
C483A
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mutation in the conserved C479xxxC483xxC486 motif of the radical-Ado-Met domain, complete loss of activity
C483S
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loss of activity
C486A
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mutation in the conserved C479xxxC483xxC486 motif of the radical-Ado-Met domain, complete loss of activity
C486S
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loss of activity
D597A
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loss of activity
D597N
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loss of activity
E532A
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mutation in a candidate GGE motif in the radical Ado-Met domain, no loss of activity
K459A
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loss of activity
R638A
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loss of activity
S595A
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loss of activity
C457S
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loss of activity
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C470S
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loss of activity
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C479A
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mutation in the conserved C479xxxC483xxC486 motif of the radical-Ado-Met domain, complete loss of activity
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C483A
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mutation in the conserved C479xxxC483xxC486 motif of the radical-Ado-Met domain, complete loss of activity
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C486A
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mutation in the conserved C479xxxC483xxC486 motif of the radical-Ado-Met domain, complete loss of activity
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C486S
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loss of activity
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D597A
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loss of activity
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E532A
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mutation in a candidate GGE motif in the radical Ado-Met domain, no loss of activity
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E550A
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mutation in a candidate GGE motif in the radical Ado-Met domain, complete loss of activity
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S595A
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loss of activity
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