TRM13_HUMAN
ID TRM13_HUMAN Reviewed; 481 AA.
AC Q9NUP7; Q5VVL0; Q9NW65;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=tRNA:m(4)X modification enzyme TRM13 homolog;
DE EC=2.1.1.225;
DE AltName: Full=Coiled-coil domain-containing protein 76;
GN Name=TRMT13; Synonyms=CCDC76;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Embryo, and Placenta;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Cervix;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP DOMAIN CHHC ZINC-FINGER.
RX PubMed=18703587; DOI=10.1093/bioinformatics/btn431;
RA Andreeva A., Tidow H.;
RT "A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA
RT modifying enzymes.";
RL Bioinformatics 24:2277-2280(2008).
RN [5]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
CC -!- FUNCTION: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro)
CC and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).
CC {ECO:0000250|UniProtKB:Q12383}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Pro) + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(4) in tRNA(Pro) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:32767, Rhea:RHEA-COMP:10397, Rhea:RHEA-COMP:10398,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000250|UniProtKB:Q12383};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-methionine = 2'-
CC O-methylcytidine(4) in tRNA(Gly)(GCC) + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:43192, Rhea:RHEA-COMP:10399, Rhea:RHEA-
CC COMP:10400, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000250|UniProtKB:Q12383};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(4) in tRNA(His) + S-adenosyl-L-methionine = 2'-O-
CC methyladenosine(4) in tRNA(His) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43196, Rhea:RHEA-COMP:10401, Rhea:RHEA-COMP:10402,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74477; EC=2.1.1.225;
CC Evidence={ECO:0000250|UniProtKB:Q12383};
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9NUP7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9NUP7-2; Sequence=VSP_018578, VSP_018579;
CC -!- SIMILARITY: Belongs to the methyltransferase TRM13 family.
CC {ECO:0000305}.
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DR EMBL; AK001149; BAA91520.1; -; mRNA.
DR EMBL; AK002081; BAA92074.1; -; mRNA.
DR EMBL; AL445928; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC075811; AAH75811.1; -; mRNA.
DR CCDS; CCDS765.1; -. [Q9NUP7-1]
DR RefSeq; NP_061956.2; NM_019083.2. [Q9NUP7-1]
DR AlphaFoldDB; Q9NUP7; -.
DR BioGRID; 119985; 8.
DR IntAct; Q9NUP7; 5.
DR STRING; 9606.ENSP00000359160; -.
DR iPTMnet; Q9NUP7; -.
DR PhosphoSitePlus; Q9NUP7; -.
DR BioMuta; TRMT13; -.
DR DMDM; 108885172; -.
DR EPD; Q9NUP7; -.
DR jPOST; Q9NUP7; -.
DR MassIVE; Q9NUP7; -.
DR MaxQB; Q9NUP7; -.
DR PaxDb; Q9NUP7; -.
DR PeptideAtlas; Q9NUP7; -.
DR PRIDE; Q9NUP7; -.
DR ProteomicsDB; 82703; -. [Q9NUP7-1]
DR ProteomicsDB; 82704; -. [Q9NUP7-2]
DR Antibodypedia; 33692; 41 antibodies from 14 providers.
DR DNASU; 54482; -.
DR Ensembl; ENST00000370141.8; ENSP00000359160.2; ENSG00000122435.11. [Q9NUP7-1]
DR Ensembl; ENST00000482437.5; ENSP00000432616.1; ENSG00000122435.11. [Q9NUP7-2]
DR GeneID; 54482; -.
DR KEGG; hsa:54482; -.
DR MANE-Select; ENST00000370141.8; ENSP00000359160.2; NM_019083.3; NP_061956.2.
DR UCSC; uc001dsv.4; human. [Q9NUP7-1]
DR CTD; 54482; -.
DR GeneCards; TRMT13; -.
DR HGNC; HGNC:25502; TRMT13.
DR HPA; ENSG00000122435; Low tissue specificity.
DR neXtProt; NX_Q9NUP7; -.
DR OpenTargets; ENSG00000122435; -.
DR PharmGKB; PA143485428; -.
DR VEuPathDB; HostDB:ENSG00000122435; -.
DR eggNOG; KOG2811; Eukaryota.
DR GeneTree; ENSGT00390000003182; -.
DR HOGENOM; CLU_027610_1_0_1; -.
DR InParanoid; Q9NUP7; -.
DR OMA; HRCSWRS; -.
DR OrthoDB; 713196at2759; -.
DR PhylomeDB; Q9NUP7; -.
DR TreeFam; TF317538; -.
DR PathwayCommons; Q9NUP7; -.
DR Reactome; R-HSA-6782315; tRNA modification in the nucleus and cytosol.
DR SignaLink; Q9NUP7; -.
DR BioGRID-ORCS; 54482; 11 hits in 1064 CRISPR screens.
DR ChiTaRS; TRMT13; human.
DR GenomeRNAi; 54482; -.
DR Pharos; Q9NUP7; Tdark.
DR PRO; PR:Q9NUP7; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; Q9NUP7; protein.
DR Bgee; ENSG00000122435; Expressed in secondary oocyte and 188 other tissues.
DR ExpressionAtlas; Q9NUP7; baseline and differential.
DR Genevisible; Q9NUP7; HS.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0106050; F:tRNA 2'-O-methyltransferase activity; IEA:InterPro.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
DR InterPro; IPR007871; Methyltransferase_TRM13.
DR InterPro; IPR039044; Trm13.
DR InterPro; IPR022776; TRM13/UPF0224_CHHC_Znf_dom.
DR InterPro; IPR021721; Znf_CCCH-type_TRM13.
DR PANTHER; PTHR12998; PTHR12998; 1.
DR Pfam; PF05206; TRM13; 1.
DR Pfam; PF11722; zf-TRM13_CCCH; 1.
DR Pfam; PF05253; zf-U11-48K; 1.
DR PROSITE; PS51800; ZF_CHHC_U11_48K; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Coiled coil; Metal-binding;
KW Methyltransferase; Reference proteome; S-adenosyl-L-methionine;
KW Transferase; tRNA processing; Zinc; Zinc-finger.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:22223895"
FT CHAIN 2..481
FT /note="tRNA:m(4)X modification enzyme TRM13 homolog"
FT /id="PRO_0000236678"
FT ZN_FING 56..83
FT /note="CHHC U11-48K-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT REGION 381..408
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 113..140
FT /evidence="ECO:0000255"
FT COMPBIAS 391..408
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 59
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 65
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:22223895"
FT VAR_SEQ 168..175
FT /note="ASILGNIE -> VCLGYSNY (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_018578"
FT VAR_SEQ 176..481
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_018579"
FT VARIANT 48
FT /note="A -> V (in dbSNP:rs687513)"
FT /id="VAR_057806"
FT CONFLICT 48
FT /note="A -> M (in Ref. 1; BAA92074 and 3; AAH75811)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 481 AA; 54247 MW; A801BFD66D6BFB5A CRC64;
MATSATSPHA PGFPAEGRCG YYVEKKKRFC RMVVAAGKRF CGEHAGAAEE EDARKRILCP
LDPKHTVYED QLAKHLKKCN SREKPKPDFY IQDINAGLRD ETEIPEQLVP ISSLSEEQLE
KLIKKLRKAS EGLNSTLKDH IMSHPALHDA LNDPKNGDSA TKHLKQQASI LGNIENLKLL
GPRRCFVEFG AGKGKLSHWV DIALKDAEKV HFILVEKVTT RFKVDGKHRK KNSVFERLQI
DIQHLCLNKI PVLREEKLPV VGIGKHLCGM ATDLALRCLV ETYAASFEER NEEPLAKRIK
NDKTEKEIYT LAKEGNEKNV PEKWNPVAGI VIALCCHHRC DWRHYVGKEY FRALGLGAVE
FHYFQRMSSW ATCGMRKTSL ETSNSTTKRQ DNQNDDSEEH DDGGYRITDD GADCLPGLLS
VEEKKKIGHL CKLLIDQGRI QYLQQKGFSP ALQYYTDPLV SLENVLLTAL PNHSSSPETT
A
