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Protein

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

Gene

TYW1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

N1-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)DescriptionActionsGraphical viewLength
Metal bindingi416Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
Metal bindingi420Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
Metal bindingi423Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi85 – 89FMNPROSITE-ProRule annotation5
Nucleotide bindingi176 – 208FMNPROSITE-ProRule annotationAdd BLAST33

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase
Biological processtRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

ReactomeiR-HSA-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):
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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

EuPathDBiHostDB:ENSG00000198874.12
HGNCiHGNC:25598 TYW1
MIMi611243 gene
neXtProtiNX_Q9NV66

Pathology & Biotechi

Organism-specific databases

DisGeNETi55253
OpenTargetsiENSG00000198874
PharmGKBiPA134940167

Polymorphism and mutation databases

DMDMi143678193

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002818261 – 732S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthaseAdd BLAST732

Proteomic databases

EPDiQ9NV66
MaxQBiQ9NV66
PaxDbiQ9NV66
PeptideAtlasiQ9NV66
PRIDEiQ9NV66
ProteomicsDBi82752
82753 [Q9NV66-2]

PTM databases

iPTMnetiQ9NV66
PhosphoSitePlusiQ9NV66

Expressioni

Gene expression databases

BgeeiENSG00000198874
CleanExiHS_TYW1
ExpressionAtlasiQ9NV66 baseline and differential
GenevisibleiQ9NV66 HS

Organism-specific databases

HPAiHPA013568
HPA014118
HPA015535
HPA043136
HPA047029
HPA047052
HPA052097

Interactioni

Protein-protein interaction databases

BioGridi120544, 42 interactors
IntActiQ9NV66, 3 interactors
STRINGi9606.ENSP00000352645

Structurei

3D structure databases

ProteinModelPortaliQ9NV66
SMRiQ9NV66
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini79 – 237Flavodoxin-likePROSITE-ProRule annotationAdd BLAST159

Sequence similaritiesi

Belongs to the TYW1 family.Curated

Phylogenomic databases

eggNOGiKOG1160 Eukaryota
COG0369 LUCA
COG0731 LUCA
GeneTreeiENSGT00510000047059
HOVERGENiHBG108623
InParanoidiQ9NV66
KOiK15449
OMAiFKDFWPR
OrthoDBiEOG091G06T8
PhylomeDBiQ9NV66
TreeFamiTF300773

Family and domain databases

Gene3Di3.20.20.70, 1 hit
3.40.50.360, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR001094 Flavdoxin-like
IPR008254 Flavodoxin/NO_synth
IPR029039 Flavoprotein-like_sf
IPR007197 rSAM
IPR013917 tRNA_wybutosine-synth
IPR034556 tRNA_wybutosine-synthase
PANTHERiPTHR13930 PTHR13930, 1 hit
PfamiView protein in Pfam
PF00258 Flavodoxin_1, 1 hit
PF04055 Radical_SAM, 1 hit
PF08608 Wyosine_form, 1 hit
PRINTSiPR00369 FLAVODOXIN
SFLDiSFLDG01071 tRNA_wybutosine-synthesizing, 1 hit
SFLDS00029 Radical_SAM, 1 hit
SUPFAMiSSF52218 SSF52218, 1 hit
PROSITEiView protein in PROSITE
PS50902 FLAVODOXIN_LIKE, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NV66-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MDPSADTWDL FSPLISLWIN RFYIYLGFAV SISLWICVQI VIKTQGKNLQ
60 70 80 90 100
EKSVPKAAQD LMTNGYVSLQ EKDIFVSGVK IFYGSQTGTA KGFATVLAEA
110 120 130 140 150
VTSLDLPVAI INLKEYDPDD HLIEEVTSKN VCVFLVATYT DGLPTESAEW
160 170 180 190 200
FCKWLEEASI DFRFGKTYLK GMRYAVFGLG NSAYASHFNK VGKNVDKWLW
210 220 230 240 250
MLGAHRVMSR GEGDCDVVKS KHGSIEADFR AWKTKFISQL QALQKGERKK
260 270 280 290 300
SCGGHCKKGK CESHQHGSEE REEGSHEQDE LHHRDTEEEE PFESSSEEEF
310 320 330 340 350
GGEDHQSLNS IVDVEDLGKI MDHVKKEKRE KEQQEEKSGL FRNMGRNEDG
360 370 380 390 400
ERRAMITPAL REALTKQGYQ LIGSHSGVKL CRWTKSMLRG RGGCYKHTFY
410 420 430 440 450
GIESHRCMET TPSLACANKC VFCWRHHTNP VGTEWRWKMD QPEMILKEAI
460 470 480 490 500
ENHQNMIKQF KGVPGVKAER FEEGMTVKHC ALSLVGEPIM YPEINRFLKL
510 520 530 540 550
LHQCKISSFL VTNAQFPAEI RNLEPVTQLY VSVDASTKDS LKKIDRPLFK
560 570 580 590 600
DFWQRFLDSL KALAVKQQRT VYRLTLVKAW NVDELQAYAQ LVSLGNPDFI
610 620 630 640 650
EVKGVTYCGE SSASSLTMAH VPWHEEVVQF VHELVDLIPE YEIACEHEHS
660 670 680 690 700
NCLLIAHRKF KIGGEWWTWI DYNRFQELIQ EYEDSGGSKT FSAKDYMART
710 720 730
PHWALFGASE RGFDPKDTRH QRKNKSKAIS GC
Length:732
Mass (Da):83,702
Last modified:April 3, 2007 - v2
Checksum:i95E8E5C3F88ADD23
GO
Isoform 2 (identifier: Q9NV66-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     368-384: GYQLIGSHSGVKLCRWT → VHAPRERRLLQTHILWN
     385-732: Missing.

Note: No experimental confirmation available.
Show »
Length:384
Mass (Da):43,700
Checksum:i43A06B3E5DFC86C6
GO

Sequence cautioni

The sequence AAH15591 differs from that shown. Reason: Frameshift at position 663.Curated
The sequence BAB14307 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti382R → M in BAB14307 (PubMed:14702039).Curated1
Sequence conflicti388L → F in BAB14307 (PubMed:14702039).Curated1
Sequence conflicti416C → Y in BAB14307 (PubMed:14702039).Curated1
Sequence conflicti543K → R in BAB14307 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_031288462G → V. Corresponds to variant dbSNP:rs2261015Ensembl.1
Natural variantiVAR_031289632H → R1 PublicationCorresponds to variant dbSNP:rs2949097Ensembl.1
Natural variantiVAR_031290671D → N1 PublicationCorresponds to variant dbSNP:rs28450001Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_024066368 – 384GYQLI…LCRWT → VHAPRERRLLQTHILWN in isoform 2. 1 PublicationAdd BLAST17
Alternative sequenceiVSP_024067385 – 732Missing in isoform 2. 1 PublicationAdd BLAST348

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001762 mRNA Translation: BAA91891.1
AK022917 mRNA Translation: BAB14307.1 Different initiation.
AC079920 Genomic DNA No translation available.
AC006480 Genomic DNA Translation: AAS07568.1
AC073089 Genomic DNA Translation: AAS07520.1
BC015591 mRNA Translation: AAH15591.1 Frameshift.
BC042156 mRNA Translation: AAH42156.1 Different termination.
BC051888 mRNA Translation: AAH51888.1
CCDSiCCDS5538.1 [Q9NV66-1]
RefSeqiNP_060734.2, NM_018264.3 [Q9NV66-1]
UniGeneiHs.520917

Genome annotation databases

EnsembliENST00000359626; ENSP00000352645; ENSG00000198874 [Q9NV66-1]
ENST00000361660; ENSP00000354795; ENSG00000198874 [Q9NV66-2]
GeneIDi55253
KEGGihsa:55253
UCSCiuc003tvn.5 human [Q9NV66-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiTYW1_HUMAN
AccessioniPrimary (citable) accession number: Q9NV66
Secondary accession number(s): Q6PJG8
, Q75MG8, Q75MN3, Q86V12, Q8IVS7, Q9H9C4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: April 3, 2007
Last modified: June 20, 2018
This is version 128 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. SIMILARITY comments
    Index of protein domains and families

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