A2RUC4 (TYW5_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA wybutosine-synthesizing protein 5
Short name=hTYW5
EC=1.14.11.-

Gene names

Name:	TYW5
Synonyms:	C2orf60

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	315 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5
Cofactor	Binds 1 Fe2+ ion per subunit. Ref.6
Pathway	tRNA modification; wybutosine-tRNA(Phe) biosynthesis. Ref.5 Ref.6
Subunit structure	Homodimer. Ref.6
Sequence similarities	Belongs to the TYW5 family. Contains 1 JmjC domain.
Sequence caution	The sequence AAH63502.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	tRNA processing
Coding sequence diversity	Alternative splicing Polymorphism
Ligand	Iron Metal-binding
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	wybutosine biosynthetic process Inferred from direct assay Ref.5Ref.6. Source: UniProtKB
Molecular_function	iron ion binding Inferred from direct assay Ref.6. 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 Inferred from direct assay Ref.5Ref.6. Source: UniProtKB oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW protein homodimerization activity Inferred from direct assay Ref.6. Source: UniProtKB tRNA binding Inferred from direct assay Ref.6. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: A2RUC4-1)

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.

Isoform 2 (identifier: A2RUC4-2)

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

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 315

315

tRNA wybutosine-synthesizing protein 5

PRO_0000309274

Regions

Domain

102 – 267

166

JmjC

Sites

Metal binding

160

1

Iron; catalytic

Metal binding

162

1

Iron; catalytic

Metal binding

235

1

Iron; catalytic

Binding site

106

1

2-oxoglutarate

Binding site

166

1

2-oxoglutarate

Binding site

175

1

2-oxoglutarate

Natural variations

Alternative sequence

1 – 163

163

Missing in isoform 2.

VSP_029106

Natural variant

50

1

S → G.
Corresponds to variant rs10497844 [ dbSNP | Ensembl ].

VAR_036926

Experimental info

Mutagenesis

108

1

R → A: Abolishes enzyme activity and ability to bind tRNA. Ref.6

Mutagenesis

149

1

R → A: Abolishes enzyme activity and ability to bind tRNA. Ref.6

Secondary structure

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315

Helix Strand Turn

Details...

Beta strand

10 – 13

4

Helix

16 – 22

7

Helix

24 – 26

3

Beta strand

30 – 34

5

Helix

40 – 43

4

Helix

46 – 53

8

Beta strand

57 – 62

6

Beta strand

76 – 81

6

Helix

82 – 90

9

Beta strand

106 – 108

3

Turn

114 – 116

3

Helix

121 – 124

4

Helix

126 – 129

4

Helix

140 – 142

3

Beta strand

143 – 151

9

Beta strand

156 – 160

5

Beta strand

163 – 170

8

Beta strand

175 – 180

6

Helix

182 – 188

7

Beta strand

194 – 196

3

Beta strand

200 – 202

3

Turn

205 – 207

3

Helix

211 – 213

3

Beta strand

216 – 221

6

Beta strand

226 – 229

4

Beta strand

234 – 241

8

Beta strand

243 – 250

8

Helix

255 – 257

3

Beta strand

263 – 265

3

Helix

270 – 286

17

Helix

291 – 308

18

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 6, 2007. Version 1. Checksum: F291C48E8CA729FE	FASTA	315	36,548
	10 20 30 40 50 60 MAGQHLPVPR LEGVSREQFM QHLYPQRKPL VLEGIDLGPC TSKWTVDYLS QVGGKKEVKI 70 80 90 100 110 120 HVAAVAQMDF ISKNFVYRTL PFDQLVQRAA EEKHKEFFVS EDEKYYLRSL GEDPRKDVAD 130 140 150 160 170 180 IRKQFPLLKG DIKFPEFFKE EQFFSSVFRI SSPGLQLWTH YDVMDNLLIQ VTGKKRVVLF 190 200 210 220 230 240 SPRDAQYLYL KGTKSEVLNI DNPDLAKYPL FSKARRYECS LEAGDVLFIP ALWFHNVISE 250 260 270 280 290 300 EFGVGVNIFW KHLPSECYDK TDTYGNKDPT AASRAAQILD RALKTLAELP EEYRDFYARR 310 MVLHIQDKAY SKNSE
	Isoform 2 [UniParc]. Checksum: 3FF012BC9E0CAED4	FASTA	152	17,526
	10 20 30 40 50 60 MDNLLIQVTG KKRVVLFSPR DAQYLYLKGT KSEVLNIDNP DLAKYPLFSK ARRYECSLEA 70 80 90 100 110 120 GDVLFIPALW FHNVISEEFG VGVNIFWKHL PSECYDKTDT YGNKDPTAAS RAAQILDRAL 130 140 150 KTLAELPEEY RDFYARRMVL HIQDKAYSKN SE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00181373.
IPI00872995.

RefSeq

NP_001034782.1. NM_001039693.2.

UniGene

Hs.204619.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

A2RUC4.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000346627.

PTM databases

PhosphoSite

A2RUC4.

Proteomic databases

PaxDb

A2RUC4.

PRIDE

A2RUC4.

Protocols and materials databases

DNASU

129450.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000354611; ENSP00000346627; ENSG00000162971.

GeneID

129450.

KEGG

hsa:129450.

UCSC

uc002uvi.4. human.
uc002uvj.4. human.

Organism-specific databases

CTD

129450.

GeneCards

GC02M200794.

H-InvDB

HIX0002719.

HGNC

HGNC:26754. TYW5.

HPA

HPA045803.

neXtProt

NX_A2RUC4.

PharmGKB

PA162379298.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG276154.

HOVERGEN

HBG096249.

InParanoid

A2RUC4.

OMA

NVFWRHL.

OrthoDB

EOG4K0QNZ.

Enzyme and pathway databases

UniPathway

UPA00375.

Gene expression databases

ArrayExpress

A2RUC4.

Bgee

A2RUC4.

CleanEx

HS_C2orf60.

Genevestigator

A2RUC4.

Family and domain databases

InterPro

IPR003347. JmjC_dom.
[Graphical view]

SMART

SM00558. JmjC. 1 hit.
[Graphical view]

PROSITE

PS51184. JMJC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

GenomeRNAi

129450.

NextBio

82587.

Entry information

Entry name

TYW5_HUMAN

Accession

Primary (citable) accession number: A2RUC4
Secondary accession number(s): B2RNE3, Q8N1R2

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 13, 2007
Last sequence update:	March 6, 2007
Last modified:	May 1, 2013
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.