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Protein

tRNA wybutosine-synthesizing protein 5

Gene

TYW5

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

tRNA hydroxylase that acts as a 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 hydroxylation of 7-(a-amino-a-carboxypropyl)wyosine (yW-72) into undermodified hydroxywybutosine (OHyW*). OHyW* being further transformed into hydroxywybutosine (OHyW) by LCMT2/TYW4. OHyW is a derivative of wybutosine found in higher eukaryotes.1 Publication

Catalytic activityi

7-(3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) + 2-oxoglutarate + O2 = 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) + succinate + CO2.

Cofactori

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per subunit.1 Publication

Pathwayi: wybutosine-tRNA(Phe) biosynthesis

This protein is involved in the pathway wybutosine-tRNA(Phe) biosynthesis, which is part of tRNA modification.2 Publications
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
Binding sitei1062-oxoglutarate1 Publication1
Metal bindingi160Iron; catalytic1
Metal bindingi162Iron; catalytic1
Binding sitei1662-oxoglutarate1 Publication1
Binding sitei1752-oxoglutarate1 Publication1
Metal bindingi235Iron; catalytic1

GO - Molecular functioni

  • iron ion binding Source: UniProtKB
  • oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • tRNA binding Source: UniProtKB

GO - Biological processi

  • tRNA modification Source: Reactome
  • wybutosine biosynthetic process Source: UniProtKB

Keywordsi

Molecular functionDioxygenase, Oxidoreductase
Biological processtRNA processing
LigandIron, Metal-binding

Enzyme and pathway databases

BRENDAi1.14.11.42. 2681.
ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA wybutosine-synthesizing protein 5 (EC:1.14.11.42)
Short name:
hTYW5
Alternative name(s):
tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-C(2))-hydroxylase
Gene namesi
Name:TYW5
Synonyms:C2orf60
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000162971.10.
HGNCiHGNC:26754. TYW5.

Subcellular locationi

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi108R → A: Abolishes enzyme activity and ability to bind tRNA. 1 Publication1
Mutagenesisi149R → A: Abolishes enzyme activity and ability to bind tRNA. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000162971.
PharmGKBiPA162379298.

Polymorphism and mutation databases

BioMutaiTYW5.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003092741 – 315tRNA wybutosine-synthesizing protein 5Add BLAST315

Proteomic databases

EPDiA2RUC4.
MaxQBiA2RUC4.
PaxDbiA2RUC4.
PRIDEiA2RUC4.

PTM databases

iPTMnetiA2RUC4.
PhosphoSitePlusiA2RUC4.

Expressioni

Gene expression databases

BgeeiENSG00000162971.
CleanExiHS_C2orf60.
ExpressionAtlasiA2RUC4. baseline and differential.
GenevisibleiA2RUC4. HS.

Organism-specific databases

HPAiHPA028294.
HPA045803.

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi126193. 10 interactors.
STRINGi9606.ENSP00000346627.

Structurei

Secondary structure

1315
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 13Combined sources4
Helixi16 – 22Combined sources7
Helixi24 – 26Combined sources3
Beta strandi30 – 34Combined sources5
Helixi40 – 43Combined sources4
Helixi46 – 53Combined sources8
Beta strandi57 – 66Combined sources10
Turni70 – 72Combined sources3
Beta strandi76 – 81Combined sources6
Helixi82 – 90Combined sources9
Beta strandi106 – 108Combined sources3
Turni114 – 116Combined sources3
Helixi121 – 124Combined sources4
Helixi126 – 129Combined sources4
Helixi140 – 142Combined sources3
Beta strandi143 – 151Combined sources9
Beta strandi156 – 160Combined sources5
Beta strandi163 – 170Combined sources8
Beta strandi175 – 180Combined sources6
Helixi182 – 188Combined sources7
Beta strandi194 – 196Combined sources3
Beta strandi200 – 202Combined sources3
Turni205 – 207Combined sources3
Helixi211 – 213Combined sources3
Beta strandi216 – 221Combined sources6
Beta strandi226 – 229Combined sources4
Beta strandi234 – 241Combined sources8
Beta strandi243 – 250Combined sources8
Helixi255 – 257Combined sources3
Beta strandi263 – 265Combined sources3
Helixi270 – 286Combined sources17
Helixi291 – 308Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3AL5X-ray2.50A/B/C/D1-315[»]
3AL6X-ray2.80A/B/C/D1-315[»]
ProteinModelPortaliA2RUC4.
SMRiA2RUC4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini102 – 267JmjCPROSITE-ProRule annotationAdd BLAST166

Sequence similaritiesi

Belongs to the TYW5 family.Curated

Phylogenomic databases

eggNOGiKOG2132. Eukaryota.
ENOG410XQDR. LUCA.
GeneTreeiENSGT00530000062914.
HOVERGENiHBG096249.
InParanoidiA2RUC4.
KOiK18066.
OMAiPLYDDRP.
OrthoDBiEOG091G0B98.
PhylomeDBiA2RUC4.
TreeFamiTF332364.

Family and domain databases

InterProiView protein in InterPro
IPR003347. JmjC_dom.
IPR029612. TYW5.
PANTHERiPTHR12461:SF55. PTHR12461:SF55. 1 hit.
SMARTiView protein in SMART
SM00558. JmjC. 1 hit.
PROSITEiView protein in PROSITE
PS51184. JMJC. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: A2RUC4-1) [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
MAGQHLPVPR LEGVSREQFM QHLYPQRKPL VLEGIDLGPC TSKWTVDYLS
60 70 80 90 100
QVGGKKEVKI HVAAVAQMDF ISKNFVYRTL PFDQLVQRAA EEKHKEFFVS
110 120 130 140 150
EDEKYYLRSL GEDPRKDVAD IRKQFPLLKG DIKFPEFFKE EQFFSSVFRI
160 170 180 190 200
SSPGLQLWTH YDVMDNLLIQ VTGKKRVVLF SPRDAQYLYL KGTKSEVLNI
210 220 230 240 250
DNPDLAKYPL FSKARRYECS LEAGDVLFIP ALWFHNVISE EFGVGVNIFW
260 270 280 290 300
KHLPSECYDK TDTYGNKDPT AASRAAQILD RALKTLAELP EEYRDFYARR
310
MVLHIQDKAY SKNSE
Length:315
Mass (Da):36,548
Last modified:March 6, 2007 - v1
Checksum:iF291C48E8CA729FE
GO
Isoform 2 (identifier: A2RUC4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-163: Missing.

Note: No experimental confirmation available.
Show »
Length:152
Mass (Da):17,526
Checksum:i3FF012BC9E0CAED4
GO

Sequence cautioni

The sequence AAH63502 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03692650S → G. Corresponds to variant dbSNP:rs10497844Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0291061 – 163Missing in isoform 2. 1 PublicationAdd BLAST163

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK095272 mRNA. Translation: BAC04517.1.
AK298977 mRNA. Translation: BAG61071.1.
AC097717 Genomic DNA. Translation: AAY24162.1.
CH471063 Genomic DNA. Translation: EAW70191.1.
BC063502 mRNA. Translation: AAH63502.1. Different initiation.
BC132835 mRNA. Translation: AAI32836.1.
BC136837 mRNA. Translation: AAI36838.1.
CCDSiCCDS42795.1. [A2RUC4-1]
RefSeqiNP_001034782.1. NM_001039693.2. [A2RUC4-1]
UniGeneiHs.204619.

Genome annotation databases

EnsembliENST00000354611; ENSP00000346627; ENSG00000162971. [A2RUC4-1]
GeneIDi129450.
KEGGihsa:129450.
UCSCiuc002uvi.5. human. [A2RUC4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiTYW5_HUMAN
AccessioniPrimary (citable) accession number: A2RUC4
Secondary accession number(s): B2RNE3, Q8N1R2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: March 6, 2007
Last modified: September 27, 2017
This is version 88 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families