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A2RUC4

- TYW5_HUMAN

UniProt

A2RUC4 - TYW5_HUMAN

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Protein

tRNA wybutosine-synthesizing protein 5

Gene

TYW5

Organism
Homo sapiens (Human)
Status
Reviewed - 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

Binds 1 Fe2+ ion per subunit.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei106 – 10612-oxoglutarate1 Publication
Metal bindingi160 – 1601Iron; catalytic
Metal bindingi162 – 1621Iron; catalytic
Binding sitei166 – 16612-oxoglutarate1 Publication
Binding sitei175 – 17512-oxoglutarate1 Publication
Metal bindingi235 – 2351Iron; catalytic

GO - Molecular functioni

  1. iron ion binding Source: UniProtKB
  2. 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
  3. protein homodimerization activity Source: UniProtKB
  4. tRNA binding Source: UniProtKB

GO - Biological processi

  1. wybutosine biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

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
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:26754. TYW5.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi108 – 1081R → A: Abolishes enzyme activity and ability to bind tRNA. 1 Publication
Mutagenesisi149 – 1491R → A: Abolishes enzyme activity and ability to bind tRNA. 1 Publication

Organism-specific databases

PharmGKBiPA162379298.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 315315tRNA wybutosine-synthesizing protein 5PRO_0000309274Add
BLAST

Proteomic databases

MaxQBiA2RUC4.
PaxDbiA2RUC4.
PRIDEiA2RUC4.

PTM databases

PhosphoSiteiA2RUC4.

Expressioni

Gene expression databases

BgeeiA2RUC4.
CleanExiHS_C2orf60.
ExpressionAtlasiA2RUC4. baseline and differential.
GenevestigatoriA2RUC4.

Organism-specific databases

HPAiHPA045803.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi126193. 10 interactions.
STRINGi9606.ENSP00000346627.

Structurei

Secondary structure

1
315
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 134Combined sources
Helixi16 – 227Combined sources
Helixi24 – 263Combined sources
Beta strandi30 – 345Combined sources
Helixi40 – 434Combined sources
Helixi46 – 538Combined sources
Beta strandi57 – 626Combined sources
Beta strandi76 – 816Combined sources
Helixi82 – 909Combined sources
Beta strandi106 – 1083Combined sources
Turni114 – 1163Combined sources
Helixi121 – 1244Combined sources
Helixi126 – 1294Combined sources
Helixi140 – 1423Combined sources
Beta strandi143 – 1519Combined sources
Beta strandi156 – 1605Combined sources
Beta strandi163 – 1708Combined sources
Beta strandi175 – 1806Combined sources
Helixi182 – 1887Combined sources
Beta strandi194 – 1963Combined sources
Beta strandi200 – 2023Combined sources
Turni205 – 2073Combined sources
Helixi211 – 2133Combined sources
Beta strandi216 – 2216Combined sources
Beta strandi226 – 2294Combined sources
Beta strandi234 – 2418Combined sources
Beta strandi243 – 2508Combined sources
Helixi255 – 2573Combined sources
Beta strandi263 – 2653Combined sources
Helixi270 – 28617Combined sources
Helixi291 – 30818Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AL5X-ray2.50A/B/C/D1-315[»]
3AL6X-ray2.80A/B/C/D1-315[»]
ProteinModelPortaliA2RUC4.
SMRiA2RUC4. Positions 1-311.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini102 – 267166JmjCPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the TYW5 family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG276154.
GeneTreeiENSGT00530000062914.
HOVERGENiHBG096249.
InParanoidiA2RUC4.
KOiK18066.
OMAiRMVLRIQ.
OrthoDBiEOG7X3QRF.
PhylomeDBiA2RUC4.
TreeFamiTF332364.

Family and domain databases

InterProiIPR003347. JmjC_dom.
IPR029612. TYW5.
[Graphical view]
PANTHERiPTHR12461:SF24. PTHR12461:SF24. 1 hit.
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

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 AAH63502.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti50 – 501S → G.
Corresponds to variant rs10497844 [ dbSNP | Ensembl ].
VAR_036926

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 163163Missing in isoform 2. 1 PublicationVSP_029106Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.4. human. [A2RUC4-1]
uc002uvj.4. human. [A2RUC4-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS42795.1. [A2RUC4-1 ]
RefSeqi NP_001034782.1. NM_001039693.2. [A2RUC4-1 ]
UniGenei Hs.204619.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3AL5 X-ray 2.50 A/B/C/D 1-315 [» ]
3AL6 X-ray 2.80 A/B/C/D 1-315 [» ]
ProteinModelPortali A2RUC4.
SMRi A2RUC4. Positions 1-311.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 126193. 10 interactions.
STRINGi 9606.ENSP00000346627.

PTM databases

PhosphoSitei A2RUC4.

Proteomic databases

MaxQBi A2RUC4.
PaxDbi A2RUC4.
PRIDEi A2RUC4.

Protocols and materials databases

DNASUi 129450.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000354611 ; ENSP00000346627 ; ENSG00000162971 . [A2RUC4-1 ]
GeneIDi 129450.
KEGGi hsa:129450.
UCSCi uc002uvi.4. human. [A2RUC4-1 ]
uc002uvj.4. human. [A2RUC4-2 ]

Organism-specific databases

CTDi 129450.
GeneCardsi GC02M200794.
H-InvDB HIX0002719.
HGNCi HGNC:26754. TYW5.
HPAi HPA045803.
neXtProti NX_A2RUC4.
PharmGKBi PA162379298.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG276154.
GeneTreei ENSGT00530000062914.
HOVERGENi HBG096249.
InParanoidi A2RUC4.
KOi K18066.
OMAi RMVLRIQ.
OrthoDBi EOG7X3QRF.
PhylomeDBi A2RUC4.
TreeFami TF332364.

Enzyme and pathway databases

UniPathwayi UPA00375 .

Miscellaneous databases

GenomeRNAii 129450.
NextBioi 82587.
PROi A2RUC4.

Gene expression databases

Bgeei A2RUC4.
CleanExi HS_C2orf60.
ExpressionAtlasi A2RUC4. baseline and differential.
Genevestigatori A2RUC4.

Family and domain databases

InterProi IPR003347. JmjC_dom.
IPR029612. TYW5.
[Graphical view ]
PANTHERi PTHR12461:SF24. PTHR12461:SF24. 1 hit.
SMARTi SM00558. JmjC. 1 hit.
[Graphical view ]
PROSITEi PS51184. JMJC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Tongue.
  2. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain and Retinoblastoma.
  5. "Expanding role of the jumonji C domain as an RNA hydroxylase."
    Noma A., Ishitani R., Kato M., Nagao A., Nureki O., Suzuki T.
    J. Biol. Chem. 285:34503-34507(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PATHWAY.
  6. "Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification."
    Kato M., Araiso Y., Noma A., Nagao A., Suzuki T., Ishitani R., Nureki O.
    Nucleic Acids Res. 39:1576-1585(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 4-311 IN COMPLEX WITH 2-OXOGLUTARATE AND NICKEL ION, PATHWAY, COFACTOR, SUBUNIT, MUTAGENESIS OF ARG-108 AND ARG-149.

Entry informationi

Entry nameiTYW5_HUMAN
AccessioniPrimary (citable) accession number: A2RUC4
Secondary accession number(s): B2RNE3, Q8N1R2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: March 6, 2007
Last modified: October 29, 2014
This is version 68 of the entry and version 1 of the sequence. [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

External Data

Dasty 3