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Protein

S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase

Gene

TYW1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity).By similarity2 Publications

Catalytic activityi

N(1)-methylguanine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + L-methionine + 5'-deoxyadenosine + CO2 + H2O.

Cofactori

[4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.1 Publication

Pathwayi: wybutosine-tRNA(Phe) biosynthesis

This protein is involved in the pathway wybutosine-tRNA(Phe) biosynthesis, which is part of tRNA modification.
View all proteins of this organism that are known to be involved in the pathway wybutosine-tRNA(Phe) biosynthesis and in tRNA modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi479Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi483Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi486Iron-sulfur (4Fe-4S-S-AdoMet)1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi211 – 215FMNPROSITE-ProRule annotation5
Nucleotide bindingi304 – 337FMNPROSITE-ProRule annotationAdd BLAST34

GO - Molecular functioni

GO - Biological processi

  • tRNA modification Source: Reactome
  • wybutosine biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:G3O-34098-MONOMER.
YEAST:G3O-34098-MONOMER.
BRENDAi4.1.3.44. 984.
ReactomeiR-SCE-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase (EC:4.1.3.44)
Alternative name(s):
tRNA wybutosine-synthesizing protein 1
Gene namesi
Name:TYW1
Ordered Locus Names:YPL207W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL207W.
SGDiS000006128. TYW1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi479C → A: Loss of function. 1 Publication1
Mutagenesisi483C → A: Loss of function. 1 Publication1
Mutagenesisi486C → A: Loss of function. 1 Publication1
Mutagenesisi532E → A: No effect. 1 Publication1
Mutagenesisi550E → A: Loss of function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002178611 – 810S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthaseAdd BLAST810

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki496Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiQ08960.
PRIDEiQ08960.

PTM databases

iPTMnetiQ08960.

Interactioni

Protein-protein interaction databases

BioGridi35978. 41 interactors.
DIPiDIP-3972N.
IntActiQ08960. 8 interactors.
MINTiMINT-537786.

Structurei

3D structure databases

ProteinModelPortaliQ08960.
SMRiQ08960.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini205 – 360Flavodoxin-likePROSITE-ProRule annotationAdd BLAST156

Sequence similaritiesi

Belongs to the TYW1 family.Curated
Contains 1 flavodoxin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00510000047059.
HOGENOMiHOG000216584.
InParanoidiQ08960.
KOiK15449.
OMAiGTTWRWV.
OrthoDBiEOG092C1CFS.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.360. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR008254. Flavodoxin/NO_synth.
IPR029039. Flavoprotein-like_dom.
IPR007197. rSAM.
IPR013917. tRNA_wybutosine-synth.
[Graphical view]
PfamiPF00258. Flavodoxin_1. 1 hit.
PF04055. Radical_SAM. 1 hit.
PF08608. Wyosine_form. 1 hit.
[Graphical view]
SUPFAMiSSF52218. SSF52218. 1 hit.
PROSITEiPS50902. FLAVODOXIN_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08960-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDGFRVAGAL VVGALTAAYL YFGGRFSIAL VIIVGYGIYC NEASGGSQDS
60 70 80 90 100
QEKLDLNKQQ KKPCCSDKKI ADGGKKTGGC CSDKKNGGGK GGGCCSSKGG
110 120 130 140 150
KKGGCCSSKG GKKGGCCSSK KNIGDNENTA TEVEKAVNYP VTVDFTEVFR
160 170 180 190 200
KPTKKRSSTP KVFSKNSSSN SRVGKKLSVS KKIGPDGLIK SALTISNETL
210 220 230 240 250
LSSQIYVLYS SLQGAASKAA KSVYDKLKEL DELTNEPKLL NLDDLSDFDD
260 270 280 290 300
YFINVPVENA LYVLVLPSYD IDCPLDYFLQ TLEENANDFR VDSFPLRKLV
310 320 330 340 350
GYTVLGLGDS ESWPEKFCYQ AKRADHWISR LGGRRIFPLG KVCMKTGGSA
360 370 380 390 400
KIDEWTSLLA ETLKDDEPII YEYDENADSE EDEEEGNGSD ELGDVEDIGG
410 420 430 440 450
KGSNGKFSGA DEIKQMVAKD SPTYKNLTKQ GYKVIGSHSG VKICRWTKNE
460 470 480 490 500
LRGKGSCYKK SLFNIASSRC MELTPSLACS SKCVFCWRHG TNPVSKNWRW
510 520 530 540 550
EVDEPEYILE NALKGHYSMI KQMRGVPGVI AERFAKAFEV RHCALSLVGE
560 570 580 590 600
PILYPHINKF IQLLHQKGIT SFLVCNAQHP EALRNIVKVT QLYVSIDAPT
610 620 630 640 650
KTELKKVDRP LYKDFWERMV ECLEILKTVQ NHQRTVFRLT LVKGFNMGDV
660 670 680 690 700
SAYADLVQRG LPGFIEVKGA TFSGSSDGNG NPLTMQNIPF YEECVKFVKA
710 720 730 740 750
FTTELQRRGL HYDLAAEHAH SNCLLIADTK FKINGEWHTH IDFDKFFVLL
760 770 780 790 800
NSGKDFTYMD YLEKTPEWAL FGNGGFAPGN TRVYRKDKKK QNKENQETTT
810
RETPLPPIPA
Length:810
Mass (Da):89,805
Last modified:November 1, 1996 - v1
Checksum:iC6A18C949B6E5F8B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73563 Genomic DNA. Translation: CAA97922.1.
Z73562 Genomic DNA. Translation: CAA97921.1.
BK006949 Genomic DNA. Translation: DAA11229.1.
PIRiS65226.
RefSeqiNP_015117.1. NM_001184021.1.

Genome annotation databases

EnsemblFungiiYPL207W; YPL207W; YPL207W.
GeneIDi855894.
KEGGisce:YPL207W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73563 Genomic DNA. Translation: CAA97922.1.
Z73562 Genomic DNA. Translation: CAA97921.1.
BK006949 Genomic DNA. Translation: DAA11229.1.
PIRiS65226.
RefSeqiNP_015117.1. NM_001184021.1.

3D structure databases

ProteinModelPortaliQ08960.
SMRiQ08960.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35978. 41 interactors.
DIPiDIP-3972N.
IntActiQ08960. 8 interactors.
MINTiMINT-537786.

PTM databases

iPTMnetiQ08960.

Proteomic databases

MaxQBiQ08960.
PRIDEiQ08960.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL207W; YPL207W; YPL207W.
GeneIDi855894.
KEGGisce:YPL207W.

Organism-specific databases

EuPathDBiFungiDB:YPL207W.
SGDiS000006128. TYW1.

Phylogenomic databases

GeneTreeiENSGT00510000047059.
HOGENOMiHOG000216584.
InParanoidiQ08960.
KOiK15449.
OMAiGTTWRWV.
OrthoDBiEOG092C1CFS.

Enzyme and pathway databases

UniPathwayiUPA00375.
BioCyciMetaCyc:G3O-34098-MONOMER.
YEAST:G3O-34098-MONOMER.
BRENDAi4.1.3.44. 984.
ReactomeiR-SCE-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).

Miscellaneous databases

PROiQ08960.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.360. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR008254. Flavodoxin/NO_synth.
IPR029039. Flavoprotein-like_dom.
IPR007197. rSAM.
IPR013917. tRNA_wybutosine-synth.
[Graphical view]
PfamiPF00258. Flavodoxin_1. 1 hit.
PF04055. Radical_SAM. 1 hit.
PF08608. Wyosine_form. 1 hit.
[Graphical view]
SUPFAMiSSF52218. SSF52218. 1 hit.
PROSITEiPS50902. FLAVODOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTYW1_YEAST
AccessioniPrimary (citable) accession number: Q08960
Secondary accession number(s): D6W3G3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 5410 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.