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Protein

tRNA:m(4)X modification enzyme TRM13 homolog

Gene

TRMT13

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

Functioni

tRNA methylase which 2'-O-methylates cytidine4 in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine4 in tRNA(His).By similarity

Catalytic activityi

S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine.
S-adenosyl-L-methionine + cytidine4 in tRNA(Pro) = S-adenosyl-L-homocysteine + 2'-O-methylcytidine4 in tRNA(Pro).
S-adenosyl-L-methionine + cytidine4 in tRNA(Gly)(GCC) = S-adenosyl-L-homocysteine + 2'-O-methylcytidine4 in tRNA(Gly)(GCC).
S-adenosyl-L-methionine + adenosine4 in tRNA(His) = S-adenosyl-L-homocysteine + 2'-O-methyladenosine4 in tRNA(His).

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri59 – 7921CHHC-typeAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA:m(4)X modification enzyme TRM13 homolog (EC:2.1.1.225)
Alternative name(s):
Coiled-coil domain-containing protein 76
Gene namesi
Name:TRMT13
Synonyms:CCDC76
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:25502. TRMT13.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA143485428.

Polymorphism and mutation databases

BioMutaiTRMT13.
DMDMi108885172.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 481480tRNA:m(4)X modification enzyme TRM13 homologPRO_0000236678Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9NUP7.
MaxQBiQ9NUP7.
PaxDbiQ9NUP7.
PRIDEiQ9NUP7.

PTM databases

iPTMnetiQ9NUP7.
PhosphoSiteiQ9NUP7.

Expressioni

Gene expression databases

BgeeiQ9NUP7.
CleanExiHS_CCDC76.
ExpressionAtlasiQ9NUP7. baseline and differential.
GenevisibleiQ9NUP7. HS.

Organism-specific databases

HPAiHPA028494.
HPA041586.

Interactioni

Protein-protein interaction databases

BioGridi119985. 4 interactions.
IntActiQ9NUP7. 1 interaction.
STRINGi9606.ENSP00000359160.

Structurei

3D structure databases

ProteinModelPortaliQ9NUP7.
SMRiQ9NUP7. Positions 53-84.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili113 – 14028Sequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the TRM13 family.Curated
Contains 1 CHHC-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri59 – 7921CHHC-typeAdd
BLAST

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiKOG2811. Eukaryota.
ENOG410Z6H8. LUCA.
GeneTreeiENSGT00390000003182.
HOGENOMiHOG000000772.
HOVERGENiHBG054828.
InParanoidiQ9NUP7.
KOiK15446.
OMAiPKHTVFK.
PhylomeDBiQ9NUP7.
TreeFamiTF317538.

Family and domain databases

InterProiIPR007871. Methyltransferase_TRM13.
IPR022776. TRM13/UPF0224_CHHC_Znf_dom.
IPR021721. Znf_CCCH-type_TRM13.
[Graphical view]
PfamiPF05206. TRM13. 1 hit.
PF11722. zf-TRM13_CCCH. 1 hit.
PF05253. zf-U11-48K. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Isoform 1 (identifier: Q9NUP7-1) [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
MATSATSPHA PGFPAEGRCG YYVEKKKRFC RMVVAAGKRF CGEHAGAAEE
60 70 80 90 100
EDARKRILCP LDPKHTVYED QLAKHLKKCN SREKPKPDFY IQDINAGLRD
110 120 130 140 150
ETEIPEQLVP ISSLSEEQLE KLIKKLRKAS EGLNSTLKDH IMSHPALHDA
160 170 180 190 200
LNDPKNGDSA TKHLKQQASI LGNIENLKLL GPRRCFVEFG AGKGKLSHWV
210 220 230 240 250
DIALKDAEKV HFILVEKVTT RFKVDGKHRK KNSVFERLQI DIQHLCLNKI
260 270 280 290 300
PVLREEKLPV VGIGKHLCGM ATDLALRCLV ETYAASFEER NEEPLAKRIK
310 320 330 340 350
NDKTEKEIYT LAKEGNEKNV PEKWNPVAGI VIALCCHHRC DWRHYVGKEY
360 370 380 390 400
FRALGLGAVE FHYFQRMSSW ATCGMRKTSL ETSNSTTKRQ DNQNDDSEEH
410 420 430 440 450
DDGGYRITDD GADCLPGLLS VEEKKKIGHL CKLLIDQGRI QYLQQKGFSP
460 470 480
ALQYYTDPLV SLENVLLTAL PNHSSSPETT A
Length:481
Mass (Da):54,247
Last modified:May 30, 2006 - v2
Checksum:iA801BFD66D6BFB5A
GO
Isoform 2 (identifier: Q9NUP7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     168-175: ASILGNIE → VCLGYSNY
     176-481: Missing.

Show »
Length:175
Mass (Da):19,615
Checksum:i6117629AED2DAE7C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti48 – 481A → M in BAA92074 (PubMed:14702039).Curated
Sequence conflicti48 – 481A → M in AAH75811 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti48 – 481A → V.
Corresponds to variant rs687513 [ dbSNP | Ensembl ].
VAR_057806

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei168 – 1758ASILGNIE → VCLGYSNY in isoform 2. 1 PublicationVSP_018578
Alternative sequencei176 – 481306Missing in isoform 2. 1 PublicationVSP_018579Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001149 mRNA. Translation: BAA91520.1.
AK002081 mRNA. Translation: BAA92074.1.
AL445928 Genomic DNA. Translation: CAH72251.1.
BC075811 mRNA. Translation: AAH75811.1.
CCDSiCCDS765.1. [Q9NUP7-1]
RefSeqiNP_061956.2. NM_019083.2. [Q9NUP7-1]
UniGeneiHs.729095.

Genome annotation databases

EnsembliENST00000370141; ENSP00000359160; ENSG00000122435. [Q9NUP7-1]
ENST00000482437; ENSP00000432616; ENSG00000122435. [Q9NUP7-2]
GeneIDi54482.
KEGGihsa:54482.
UCSCiuc001dsv.4. human. [Q9NUP7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001149 mRNA. Translation: BAA91520.1.
AK002081 mRNA. Translation: BAA92074.1.
AL445928 Genomic DNA. Translation: CAH72251.1.
BC075811 mRNA. Translation: AAH75811.1.
CCDSiCCDS765.1. [Q9NUP7-1]
RefSeqiNP_061956.2. NM_019083.2. [Q9NUP7-1]
UniGeneiHs.729095.

3D structure databases

ProteinModelPortaliQ9NUP7.
SMRiQ9NUP7. Positions 53-84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119985. 4 interactions.
IntActiQ9NUP7. 1 interaction.
STRINGi9606.ENSP00000359160.

PTM databases

iPTMnetiQ9NUP7.
PhosphoSiteiQ9NUP7.

Polymorphism and mutation databases

BioMutaiTRMT13.
DMDMi108885172.

Proteomic databases

EPDiQ9NUP7.
MaxQBiQ9NUP7.
PaxDbiQ9NUP7.
PRIDEiQ9NUP7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000370141; ENSP00000359160; ENSG00000122435. [Q9NUP7-1]
ENST00000482437; ENSP00000432616; ENSG00000122435. [Q9NUP7-2]
GeneIDi54482.
KEGGihsa:54482.
UCSCiuc001dsv.4. human. [Q9NUP7-1]

Organism-specific databases

CTDi54482.
GeneCardsiTRMT13.
H-InvDBHIX0000813.
HGNCiHGNC:25502. TRMT13.
HPAiHPA028494.
HPA041586.
neXtProtiNX_Q9NUP7.
PharmGKBiPA143485428.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2811. Eukaryota.
ENOG410Z6H8. LUCA.
GeneTreeiENSGT00390000003182.
HOGENOMiHOG000000772.
HOVERGENiHBG054828.
InParanoidiQ9NUP7.
KOiK15446.
OMAiPKHTVFK.
PhylomeDBiQ9NUP7.
TreeFamiTF317538.

Enzyme and pathway databases

ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Miscellaneous databases

GenomeRNAii54482.
NextBioi56803.
PROiQ9NUP7.

Gene expression databases

BgeeiQ9NUP7.
CleanExiHS_CCDC76.
ExpressionAtlasiQ9NUP7. baseline and differential.
GenevisibleiQ9NUP7. HS.

Family and domain databases

InterProiIPR007871. Methyltransferase_TRM13.
IPR022776. TRM13/UPF0224_CHHC_Znf_dom.
IPR021721. Znf_CCCH-type_TRM13.
[Graphical view]
PfamiPF05206. TRM13. 1 hit.
PF11722. zf-TRM13_CCCH. 1 hit.
PF05253. zf-U11-48K. 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] (ISOFORMS 1 AND 2).
    Tissue: Embryo and Placenta.
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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] (ISOFORM 1).
    Tissue: Cervix.
  4. "A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes."
    Andreeva A., Tidow H.
    Bioinformatics 24:2277-2280(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN CHHC ZINC-FINGER.
  5. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  6. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiTRM13_HUMAN
AccessioniPrimary (citable) accession number: Q9NUP7
Secondary accession number(s): Q5VVL0, Q9NW65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: May 30, 2006
Last modified: April 13, 2016
This is version 109 of the entry and version 2 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 1
    Human chromosome 1: 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. 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.