Top Level Name

  ⌊ Superfamily (core) Radical SAM

    ⌊ Subgroup tRNA wybutosine-synthesizing

     ⌊ Family tRNA wybutosine-synthesizing

  ⌊ FunctionalDomain tRNA wyosine derivatives biosynthesis protein Taw1 (ID 381178)

Superfamily Assignment Evidence Code(s) FSM PubMed:17881823
Family Assignment Evidence Code CFM IES PubMed:17881823
This entry was last updated onJune 10, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Pyrococcus horikoshii Taxon ID: 53953 159795643
Pyrococcus horikoshii OT3 Taxon ID: 70601 74571635 URP
Pyrococcus horikoshii OT3 Taxon ID: 70601 3258136 URP

Uniprot

Protein NameAccessionEC Number Identifier
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase {ECO:0000255|HAMAP-Rule:MF_01921} O59412 TYW1_PYRHO (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 342 | Length of Functional Domain: 321

1       10        20        30        40        50        60

MMEMITIKPGKITVQANPNMPKEVAELFRKQHYEIVGRHSGVKLCHWLKKSLTEGRFCYK
QKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRK
LLIGYKGNPKVDKKKFEEAWNPTHAAISLSGEPMLYPYMGDLVEEFHKRGFTTFIVTNGT
IPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERILRFLELMRDLPTRTV
VRLTLVKGENMHSPEKYAKLILKARPMFVEAKAYMFVGYSRNRLTINNMPSHQDIREFAE
ALVKHLPGYHIEDEYEPSRVVLIMRDDVDPQGTGVEGRFIKH
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues
Superfamily CAR This EFD conserves 3/3 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
81 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
85 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
88 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
Subgroup CAR This EFD conserves 5/5 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
60 Lys (K) side chain Nucleophile
Notes: Lys postulated to be a catalytic nucleophile that forms a Schiff base with the pyruvate. 		covalent catalysis -- reactant IDA PubMed:17881823 PubMed:17727881
81 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:17881823 PubMed:17727881
85 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:17881823 PubMed:17727881
88 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:17881823 PubMed:17727881
242 Arg (R) side chain Steric steric role -- spectator IDA PubMed:17881823 PubMed:17727881
Family CAR This EFD conserves 5/5 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
60 Lys (K) side chain Nucleophile
Notes: Lys postulated to be a catalytic nucleophile that forms a Schiff base with the pyruvate. 		covalent catalysis -- reactant IDA PubMed:17881823 PubMed:17727881
81 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:17881823 PubMed:17727881
85 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:17881823 PubMed:17727881
88 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:17881823 PubMed:17727881
242 Arg (R) side chain Steric
Notes: Holds the N-methylguanosine in the correct orientation for the reaction to occur. 		steric role -- spectator IDA PubMed:17881823 PubMed:17727881

Catalyzed Reaction

tRNA 4-demethylwyosine synthase (AdoMet-dependent)

+ + + + + +
N(1)-methylguanosine 5'-monophosphate(1-) residue
73542		 pyruvate
15361		 S-adenosyl-L-methionine zwitterion
59789		 4-demethylwyosine 5'-monophosphate(1-) residue
64315		 5'-deoxyadenosine
17319		 L-methionine zwitterion
57844		 carbon dioxide
16526		 water
15377

EC: 4.1.3.44 | IntEnz: 4.1.3.44 | Kegg: 4.1.3.44 | BioCyc: 4.1.3.44 | BRENDA: 4.1.3.44

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
2YX0 Crystal Structure Of P. Horikoshii Tyw1 Radical Sam Enzyme 3 2.21 CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
May 14, 2014, 3:30 a.m. update curation agent holliday setDomainBoundaries.py
update domain end position 342 332
update domain start position 1 6
July 15, 2014, 5:17 a.m. update domain end position 332 330
update domain start position 6 8
Oct. 15, 2016, 5:10 a.m. update domain start position 8 10
EC number assigned by UniProtKB accession ID.