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Information on EC 4.1.3.44 - tRNA 4-demethylwyosine synthase (AdoMet-dependent) and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q57705

for references in articles please use BRENDA:EC4.1.3.44
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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.3 Oxo-acid-lyases
                4.1.3.44 tRNA 4-demethylwyosine synthase (AdoMet-dependent)
IUBMB Comments
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 . 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.
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Methanocaldococcus jannaschii
UNIPROT: Q57705
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The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Synonyms
ypl207w, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tRNA wyosine derivatives biosynthesis protein Taw1
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4-demethylwyosine synthase
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PATHWAY SOURCE
PATHWAYS
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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.
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
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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ir
additional information
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the conserved Lys residue forms a Schiff base with pyruvate. Reductive cleavage of SAM leads to formation of dAdo radical, which propagates the radical to the m1G generating a substrate radical. Radical addition to C-2 of pyruvate followed by homolytic scission of the C-1-C-2 bond would generate an intermediate, which through transimmination and subsequent deprotonation, forms imG-14. The resulting formyl radical can either acquire an H-atom or undergo reduction and protonation to produce formate. Alternatively, oxidation of the formyl radical would generate CO2
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?
NATURAL SUBSTRATE
NATURAL 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
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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ir
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
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[4Fe-4S]-center
S-adenosyl-L-methionine
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-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, using 100 mM KH2PO4/Na2HPO4 pH 6.2, 10% (w/v) PEG 3000
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C195S
the mutant shows reduced activity compared tot he wild type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, butyl Sepharose column chromatography, and HiTrap chelating column chromatography
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
ammonium sulfate precipitation, HiTrap chealting column chromatography, and butyl Sepharose column chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Young, A.P.; Bandarian, V.
Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine
Biochemistry
50
10573-10575
2011
Methanocaldococcus jannaschii (Q57705), Methanocaldococcus jannaschii ATCC 43067 (Q57705)
Manually annotated by BRENDA team
Suzuki, Y.; Noma, A.; Suzuki, T.; Senda, M.; Senda, T.; Ishitani, R.; Nureki, O.
Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA
J. Mol. Biol.
372
1204-1214
2007
Methanocaldococcus jannaschii (Q57705), Methanocaldococcus jannaschii DSM 2661 (Q57705), Saccharomyces cerevisiae (Q08960), Saccharomyces cerevisiae ATCC 204508 (Q08960)
Manually annotated by BRENDA team
Young, A.; Bandarian, V.
Mechanistic studies of the radical S-adenosyl-L-methionine enzyme 4-demethylwyosine synthase reveal the site of hydrogen atom abstraction
Biochemistry
54
3569-3572
2015
Methanocaldococcus jannaschii
-
Manually annotated by BRENDA team
Kathirvelu, V.; Perche-Letuvee, P.; Latour, J.; Atta, M.; Forouhar, F.; Gambarelli, S.; Garcia-Serres, R.
Spectroscopic evidence for cofactor-substrate interaction in the radical-SAM enzyme TYW1
Dalton Trans.
46
13211-13219
2017
Methanocaldococcus jannaschii (Q57705)
Manually annotated by BRENDA team
Grell, T.; Young, A.; Drennan, C.; Bandarian, V.
Biochemical and structural characterization of a Schiff Base in the radical-mediated biosynthesis of 4-demethylwyosine by TYW1
J. Am. Chem. Soc.
140
6842-6852
2018
Methanocaldococcus jannaschii (Q57705), Methanocaldococcus jannaschii DSM 2661 (Q57705)
Manually annotated by BRENDA team