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Protein

tRNA wybutosine-synthesizing protein 2 homolog

Gene

TRMT12

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent transferase 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 transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to the C-7 position of 4-demethylwyosine (imG-14) to produce wybutosine-86.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + 4-demethylwyosine(37) in tRNA(Phe) = S-methyl-5'-thioadenosine + 7-((3S)-3-amino-3-carboxypropyl)-4-demethylwyosine(37) in tRNA(Phe).1 Publication

Pathwayi: wybutosine-tRNA(Phe) biosynthesis

This protein is involved in the pathway wybutosine-tRNA(Phe) biosynthesis, which is part of tRNA modification.1 Publication
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
Binding sitei218 – 2181S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei225 – 2251S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei265 – 2651S-adenosyl-L-methioninePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.5.1.114. 2681.
ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA wybutosine-synthesizing protein 2 homolog (EC:2.5.1.114)
Short name:
tRNA-yW-synthesizing protein 2
Alternative name(s):
tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase
Gene namesi
Name:TRMT12
Synonyms:TRM12, TYW2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 8

Organism-specific databases

HGNCiHGNC:26091. TRMT12.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi225 – 2251K → A: Lack of activity. 1 Publication
Mutagenesisi242 – 2421Y → A: Does not affect activity. 1 Publication
Mutagenesisi248 – 2481F → A: Does not affect activity. 1 Publication
Mutagenesisi265 – 2651E → A: Lack of activity. 1 Publication
Mutagenesisi293 – 2931D → A: Does not affect activity. 1 Publication

Organism-specific databases

PharmGKBiPA142670700.

Polymorphism and mutation databases

BioMutaiTRMT12.
DMDMi74726289.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 448448tRNA wybutosine-synthesizing protein 2 homologPRO_0000281836Add
BLAST

Proteomic databases

EPDiQ53H54.
MaxQBiQ53H54.
PaxDbiQ53H54.
PeptideAtlasiQ53H54.
PRIDEiQ53H54.

Expressioni

Gene expression databases

BgeeiQ53H54.
CleanExiHS_TRMT12.
ExpressionAtlasiQ53H54. baseline and differential.
GenevisibleiQ53H54. HS.

Organism-specific databases

HPAiHPA023939.
HPA053051.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
LNX1Q8TBB13EBI-10242598,EBI-739832

Protein-protein interaction databases

BioGridi120368. 5 interactions.
IntActiQ53H54. 1 interaction.
STRINGi9606.ENSP00000329858.

Structurei

3D structure databases

ProteinModelPortaliQ53H54.
SMRiQ53H54. Positions 125-339.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni293 – 2942S-adenosyl-L-methionine bindingPROSITE-ProRule annotation

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1227. Eukaryota.
COG2520. LUCA.
GeneTreeiENSGT00390000006078.
HOGENOMiHOG000294185.
HOVERGENiHBG108624.
InParanoidiQ53H54.
KOiK07055.
OMAiHFGDNRK.
PhylomeDBiQ53H54.
TreeFamiTF314137.

Family and domain databases

Gene3Di3.40.50.150. 2 hits.
InterProiIPR030382. MeTrfase_TRM5/TYW2.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF02475. Met_10. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 2 hits.
PROSITEiPS51684. SAM_MT_TRM5_TYW2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q53H54-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRENVVVSNM ERESGKPVAV VAVVTEPWFT QRYREYLQRQ KLFDTQHRVE
60 70 80 90 100
KMPDGSVALP VLGETLPEQH LQELRNRVAP GSPCMLTQLP DPVPSKRAQG
110 120 130 140 150
CSPAQKLCLE VSRWVEGRGV KWSAELEADL PRSWQRHGNL LLLSEDCFQA
160 170 180 190 200
KQWKNLGPEL WETVALALGV QRLAKRGRVS PDGTRTPAVT LLLGDHGWVE
210 220 230 240 250
HVDNGIRYKF DVTQCMFSFG NITEKLRVAS LSCAGEVLVD LYAGIGYFTL
260 270 280 290 300
PFLVHAGAAF VHACEWNPHA VVALRNNLEI NGVADRCQIH FGDNRKLKLS
310 320 330 340 350
NIADRVILGL IPSSEEGWPI ACQVLRQDAG GILHIHQNVE SFPGKNLQAL
360 370 380 390 400
GVSKVEKEHW LYPQQITTNQ WKNGATRDSR GKMLSPATKP EWQRWAESAE
410 420 430 440
TRIATLLQQV HGKPWKTQIL HIQPVKSYAP HVDHIVLDLE CCPCPSVG
Length:448
Mass (Da):50,236
Last modified:May 24, 2005 - v1
Checksum:i5E66C20AF26C4B5F
GO

Sequence cautioni

The sequence AAH03057.2 differs from that shown.Contaminating sequence. Potential poly-A sequence starting in position 371.Curated
The sequence AAH03057.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti342 – 3421F → S in BAA91374 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti28 – 281W → R.1 Publication
Corresponds to variant rs3812475 [ dbSNP | Ensembl ].
VAR_031291

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000779 mRNA. Translation: BAA91374.1.
AK222727 mRNA. Translation: BAD96447.1.
BC003057 mRNA. Translation: AAH03057.2. Sequence problems.
BC011713 mRNA. Translation: AAH11713.1.
CCDSiCCDS6349.1.
RefSeqiNP_060426.2. NM_017956.3.
UniGeneiHs.9925.

Genome annotation databases

EnsembliENST00000328599; ENSP00000329858; ENSG00000183665.
GeneIDi55039.
KEGGihsa:55039.
UCSCiuc003yra.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000779 mRNA. Translation: BAA91374.1.
AK222727 mRNA. Translation: BAD96447.1.
BC003057 mRNA. Translation: AAH03057.2. Sequence problems.
BC011713 mRNA. Translation: AAH11713.1.
CCDSiCCDS6349.1.
RefSeqiNP_060426.2. NM_017956.3.
UniGeneiHs.9925.

3D structure databases

ProteinModelPortaliQ53H54.
SMRiQ53H54. Positions 125-339.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120368. 5 interactions.
IntActiQ53H54. 1 interaction.
STRINGi9606.ENSP00000329858.

Polymorphism and mutation databases

BioMutaiTRMT12.
DMDMi74726289.

Proteomic databases

EPDiQ53H54.
MaxQBiQ53H54.
PaxDbiQ53H54.
PeptideAtlasiQ53H54.
PRIDEiQ53H54.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000328599; ENSP00000329858; ENSG00000183665.
GeneIDi55039.
KEGGihsa:55039.
UCSCiuc003yra.5. human.

Organism-specific databases

CTDi55039.
GeneCardsiTRMT12.
HGNCiHGNC:26091. TRMT12.
HPAiHPA023939.
HPA053051.
MIMi611244. gene.
neXtProtiNX_Q53H54.
PharmGKBiPA142670700.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1227. Eukaryota.
COG2520. LUCA.
GeneTreeiENSGT00390000006078.
HOGENOMiHOG000294185.
HOVERGENiHBG108624.
InParanoidiQ53H54.
KOiK07055.
OMAiHFGDNRK.
PhylomeDBiQ53H54.
TreeFamiTF314137.

Enzyme and pathway databases

UniPathwayiUPA00375.
BRENDAi2.5.1.114. 2681.
ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).

Miscellaneous databases

ChiTaRSiTRMT12. human.
GeneWikiiTRMT12.
GenomeRNAii55039.
PROiQ53H54.
SOURCEiSearch...

Gene expression databases

BgeeiQ53H54.
CleanExiHS_TRMT12.
ExpressionAtlasiQ53H54. baseline and differential.
GenevisibleiQ53H54. HS.

Family and domain databases

Gene3Di3.40.50.150. 2 hits.
InterProiIPR030382. MeTrfase_TRM5/TYW2.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF02475. Met_10. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 2 hits.
PROSITEiPS51684. SAM_MT_TRM5_TYW2. 1 hit.
[Graphical view]
ProtoNetiSearch...

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].
    Tissue: Colon.
  2. Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
    Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Colon.
  3. "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], VARIANT ARG-28.
    Tissue: Ovary and Skin.
  4. "Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA."
    Rodriguez V., Vasudevan S., Noma A., Carlson B.A., Green J.E., Suzuki T., Chandrasekharappa S.C.
    PLoS ONE 7:E39297-E39297(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, PATHWAY, MUTAGENESIS OF LYS-225; TYR-242; PHE-248; GLU-265 AND ASP-293.

Entry informationi

Entry nameiTYW2_HUMAN
AccessioniPrimary (citable) accession number: Q53H54
Secondary accession number(s): Q6PKB9, Q96F21, Q9NWK6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: May 24, 2005
Last modified: June 8, 2016
This is version 86 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: 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

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.