Top Level Name

  ⌊ Superfamily (core) Radical SAM

    ⌊ Subgroup tRNA wybutosine-synthesizing

     ⌊ Family tRNA wybutosine-synthesizing

  ⌊ FunctionalDomain tRNA wybutosine-synthesizing protein (ID 410654)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code IEA
This entry was last updated onJune 10, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Pyrococcus abyssi GE5 Taxon ID: 272844 74547469 URP
Pyrococcus abyssi GE5 Taxon ID: 272844 5457900 URP

Uniprot

Protein NameAccessionEC Number Identifier
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase {ECO:0000255|HAMAP-Rule:MF_01921} Q9V1F9 TYW1_PYRAB (Swiss-Prot)

Sequence

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

1       10        20        30        40        50        60

MREMITIKPGKITVQANPNMPEEVANLFRKQHYEIVGRHSGVKLCHWLKKSLTEGRFCYK
QKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMETFLGTELPQPWDDPEFIVEESIKAQRK
LLIGYKGNPKVDKKKFEEAWEPKHAAISLSGEPMLYPYMGDLVEEFHKRGFTTFIVTNGT
VPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERIMRFLELMRDLPTRTV
VRLTLVKGENMHSPEKYAKLILKARPMFVEAKAYMFVGYSRNRLTINNMPSHQDIREFAE
ALVKHLPGYHIEDEYEPSRVVLIMRDDVDPQGTGVNGRFIKH
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

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, 2:58 a.m. update curation agent holliday setDomainBoundaries.py
update domain end position 342 333
update domain start position 1 6
July 15, 2014, 6:01 a.m. update domain end position 333 330
update domain start position 6 8
Oct. 15, 2016, 6:06 a.m. update domain start position 8 10
EC number assigned by UniProtKB accession ID.