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Protein

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

Gene

tyw1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Probable 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 similarity

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] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.By similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi414 – 4141Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi418 – 4181Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi421 – 4211Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi85 – 895FMNPROSITE-ProRule annotation
Nucleotide bindingi176 – 20833FMNPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase (EC:4.1.3.44)
Alternative name(s):
Radical S-adenosyl methionine and flavodoxin domain-containing protein 1
tRNA wybutosine-synthesizing protein 1 homolog
tRNA-yW-synthesizing protein
Gene namesi
Name:tyw1
Synonyms:rsafd1
ORF Names:zgc:153368
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-060929-688. tyw1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 730730S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthasePRO_0000281830Add
BLAST

Proteomic databases

PaxDbiQ08C92.
PRIDEiQ08C92.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000117225.

Structurei

3D structure databases

ProteinModelPortaliQ08C92.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini79 – 237159Flavodoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1160. Eukaryota.
COG0369. LUCA.
COG0731. LUCA.
HOGENOMiHOG000216584.
HOVERGENiHBG108623.
InParanoidiQ08C92.
KOiK15449.
PhylomeDBiQ08C92.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.360. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001094. Flavdoxin-like.
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]
PRINTSiPR00369. FLAVODOXIN.
SUPFAMiSSF52218. SSF52218. 1 hit.
PROSITEiPS50902. FLAVODOXIN_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08C92-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGVLNDVRD YTEGYLQVLW QNRLYVYSTA AVLIGVWFTV NMLFKKKKMV
60 70 80 90 100
HPVSPLASKS VKKQEPASEA KKVIYVSGVK VFYGSQTGTA KGFAKELAED
110 120 130 140 150
VIAQGIQCEV IDMKDFDPED RLAEECTSKI ICVFLVATYT DGQPTESAEW
160 170 180 190 200
FCKWLEEAST DFRYGKTYLK GMRYAVFGLG NSVYVGHFNT VSKSIDKWLW
210 220 230 240 250
MLSAARIMTR GEGDCNVVKS RHGSVQADFQ VWKGKFLNRL QALAKGEKKA
260 270 280 290 300
CSGNCKKASC KNKKKHKEEA EDNHSLAEKN NSEEELMESS SDEESSSEDE
310 320 330 340 350
KSHGSVIDME DLGNVMNHMK KAKQRMEEDE EDSQRVKQNG ERKSECEEER
360 370 380 390 400
REMITPALRD SLTKQGYKLI GSHSGVKLRR WTKSMLRGRG GCYKHTFYGI
410 420 430 440 450
ESHRCMETTP SLACANKCVF CWRHHTNPVG TEWRWKMDPA EKIIQEAMEN
460 470 480 490 500
HRNMIRQFRG VPGVRPERFE EGLTVKHCAL SLVGEPIMYP EINSFLKLLH
510 520 530 540 550
QQNISSFLVT NAQFPEEIRS LVPVTQLYVS VDASTKDSLK KIDRPLFKDF
560 570 580 590 600
WQRFLDSLRA LGEKQQRTVY RLTLVKAWNV DELKAYADLI ALGQPDFIEV
610 620 630 640 650
KGVTYCGESS ASSLTMANVP WHEEVIYFVQ QLANLLPDYE IACEHEHSNC
660 670 680 690 700
LLLANHKFKV DGEWWTWIDY ERFQELIQQY EESGGTKNFS AMDYMAKTPS
710 720 730
WAVFGAGERG FDPTDTRFQR KNKTKDISGC
Length:730
Mass (Da):83,549
Last modified:October 31, 2006 - v1
Checksum:i4ADA626B453E5F56
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC124331 mRNA. Translation: AAI24332.1.
RefSeqiNP_001070624.1. NM_001077156.1.
UniGeneiDr.104463.

Genome annotation databases

GeneIDi562076.
KEGGidre:562076.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC124331 mRNA. Translation: AAI24332.1.
RefSeqiNP_001070624.1. NM_001077156.1.
UniGeneiDr.104463.

3D structure databases

ProteinModelPortaliQ08C92.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000117225.

Proteomic databases

PaxDbiQ08C92.
PRIDEiQ08C92.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi562076.
KEGGidre:562076.

Organism-specific databases

CTDi55253.
ZFINiZDB-GENE-060929-688. tyw1.

Phylogenomic databases

eggNOGiKOG1160. Eukaryota.
COG0369. LUCA.
COG0731. LUCA.
HOGENOMiHOG000216584.
HOVERGENiHBG108623.
InParanoidiQ08C92.
KOiK15449.
PhylomeDBiQ08C92.

Enzyme and pathway databases

UniPathwayiUPA00375.

Miscellaneous databases

NextBioi20884237.
PROiQ08C92.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.360. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001094. Flavdoxin-like.
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]
PRINTSiPR00369. FLAVODOXIN.
SUPFAMiSSF52218. SSF52218. 1 hit.
PROSITEiPS50902. FLAVODOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Ovary.

Entry informationi

Entry nameiTYW1_DANRE
AccessioniPrimary (citable) accession number: Q08C92
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: October 31, 2006
Last modified: January 20, 2016
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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

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.