THUM1_HUMAN
ID THUM1_HUMAN Reviewed; 353 AA.
AC Q9NXG2; Q9BWC3;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=THUMP domain-containing protein 1;
GN Name=THUMPD1;
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].
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=10493829; DOI=10.1006/geno.1999.5927;
RA Loftus B.J., Kim U.-J., Sneddon V.P., Kalush F., Brandon R., Fuhrmann J.,
RA Mason T., Crosby M.L., Barnstead M., Cronin L., Mays A.D., Cao Y., Xu R.X.,
RA Kang H.-L., Mitchell S., Eichler E.E., Harris P.C., Venter J.C.,
RA Adams M.D.;
RT "Genome duplications and other features in 12 Mb of DNA sequence from human
RT chromosome 16p and 16q.";
RL Genomics 60:295-308(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung;
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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-86 AND SER-88, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
RA Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.;
RT "Global, in vivo, and site-specific phosphorylation dynamics in signaling
RT networks.";
RL Cell 127:635-648(2006).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=T-cell;
RX PubMed=19367720; DOI=10.1021/pr800500r;
RA Carrascal M., Ovelleiro D., Casas V., Gay M., Abian J.;
RT "Phosphorylation analysis of primary human T lymphocytes using sequential
RT IMAC and titanium oxide enrichment.";
RL J. Proteome Res. 7:5167-5176(2008).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-86 AND SER-88, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=18318008; DOI=10.1002/pmic.200700884;
RA Han G., Ye M., Zhou H., Jiang X., Feng S., Jiang X., Tian R., Wan D.,
RA Zou H., Gu J.;
RT "Large-scale phosphoproteome analysis of human liver tissue by enrichment
RT and fractionation of phosphopeptides with strong anion exchange
RT chromatography.";
RL Proteomics 8:1346-1361(2008).
RN [8]
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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-86 AND SER-88, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-86 AND SER-88, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [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 [11]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [12]
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=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-86; SER-88; SER-119 AND
RP SER-270, AND 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).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-79; SER-86 AND SER-88, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [15]
RP FUNCTION, AND INTERACTION WITH NAT10.
RX PubMed=25653167; DOI=10.1093/nar/gkv075;
RA Sharma S., Langhendries J.L., Watzinger P., Koetter P., Entian K.D.,
RA Lafontaine D.L.;
RT "Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine
RT acetyltransferases that modify tRNAs assisted by the adaptor
RT Tan1/THUMPD1.";
RL Nucleic Acids Res. 43:2242-2258(2015).
RN [16]
RP STRUCTURE BY NMR OF 170-254.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of the THUMP domain of THUMP domain-containing protein
RT 1.";
RL Submitted (SEP-2006) to the PDB data bank.
RN [17]
RP VARIANT 236-GLN--SER-353 DEL.
RX PubMed=30237576; DOI=10.1038/s41436-018-0138-x;
RA Maddirevula S., Alzahrani F., Al-Owain M., Al Muhaizea M.A., Kayyali H.R.,
RA AlHashem A., Rahbeeni Z., Al-Otaibi M., Alzaidan H.I., Balobaid A.,
RA El Khashab H.Y., Bubshait D.K., Faden M., Yamani S.A., Dabbagh O.,
RA Al-Mureikhi M., Jasser A.A., Alsaif H.S., Alluhaydan I., Seidahmed M.Z.,
RA Alabbasi B.H., Almogarri I., Kurdi W., Akleh H., Qari A., Al Tala S.M.,
RA Alhomaidi S., Kentab A.Y., Salih M.A., Chedrawi A., Alameer S., Tabarki B.,
RA Shamseldin H.E., Patel N., Ibrahim N., Abdulwahab F., Samira M., Goljan E.,
RA Abouelhoda M., Meyer B.F., Hashem M., Shaheen R., AlShahwan S.,
RA Alfadhel M., Ben-Omran T., Al-Qattan M.M., Monies D., Alkuraya F.S.;
RT "Autozygome and high throughput confirmation of disease genes candidacy.";
RL Genet. Med. 21:736-742(2019).
CC -!- FUNCTION: Functions as a tRNA-binding adapter to mediate NAT10-
CC dependent tRNA acetylation (PubMed:25653167).
CC {ECO:0000269|PubMed:25653167}.
CC -!- SUBUNIT: Interacts with NAT10 (PubMed:25653167).
CC {ECO:0000269|PubMed:25653167}.
CC -!- INTERACTION:
CC Q9NXG2; Q9H0A0: NAT10; NbExp=2; IntAct=EBI-5462248, EBI-876527;
CC -!- SIMILARITY: Belongs to the THUMPD1 family. {ECO:0000305}.
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DR EMBL; AK000281; BAA91050.1; -; mRNA.
DR EMBL; AC004381; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC000448; AAH00448.1; -; mRNA.
DR CCDS; CCDS10588.1; -.
DR RefSeq; NP_001291479.1; NM_001304550.1.
DR RefSeq; NP_060206.2; NM_017736.4.
DR RefSeq; XP_016878922.1; XM_017023433.1.
DR PDB; 2DIR; NMR; -; A=170-254.
DR PDBsum; 2DIR; -.
DR AlphaFoldDB; Q9NXG2; -.
DR SMR; Q9NXG2; -.
DR BioGRID; 120762; 46.
DR IntAct; Q9NXG2; 11.
DR MINT; Q9NXG2; -.
DR STRING; 9606.ENSP00000370741; -.
DR GlyGen; Q9NXG2; 2 sites, 1 O-linked glycan (2 sites).
DR iPTMnet; Q9NXG2; -.
DR PhosphoSitePlus; Q9NXG2; -.
DR BioMuta; THUMPD1; -.
DR DMDM; 61248576; -.
DR EPD; Q9NXG2; -.
DR jPOST; Q9NXG2; -.
DR MassIVE; Q9NXG2; -.
DR MaxQB; Q9NXG2; -.
DR PaxDb; Q9NXG2; -.
DR PeptideAtlas; Q9NXG2; -.
DR PRIDE; Q9NXG2; -.
DR ProteomicsDB; 83094; -.
DR Antibodypedia; 25603; 134 antibodies from 23 providers.
DR DNASU; 55623; -.
DR Ensembl; ENST00000381337.6; ENSP00000370741.2; ENSG00000066654.14.
DR Ensembl; ENST00000396083.7; ENSP00000379392.2; ENSG00000066654.14.
DR Ensembl; ENST00000636554.1; ENSP00000490841.1; ENSG00000066654.14.
DR GeneID; 55623; -.
DR KEGG; hsa:55623; -.
DR MANE-Select; ENST00000396083.7; ENSP00000379392.2; NM_017736.5; NP_060206.2.
DR UCSC; uc002dho.5; human.
DR CTD; 55623; -.
DR DisGeNET; 55623; -.
DR GeneCards; THUMPD1; -.
DR HGNC; HGNC:23807; THUMPD1.
DR HPA; ENSG00000066654; Low tissue specificity.
DR MIM; 616662; gene.
DR neXtProt; NX_Q9NXG2; -.
DR OpenTargets; ENSG00000066654; -.
DR PharmGKB; PA134983093; -.
DR VEuPathDB; HostDB:ENSG00000066654; -.
DR eggNOG; KOG3943; Eukaryota.
DR GeneTree; ENSGT00390000002365; -.
DR HOGENOM; CLU_039352_0_0_1; -.
DR InParanoid; Q9NXG2; -.
DR OMA; ECVFFMK; -.
DR OrthoDB; 1478461at2759; -.
DR PhylomeDB; Q9NXG2; -.
DR TreeFam; TF313884; -.
DR PathwayCommons; Q9NXG2; -.
DR Reactome; R-HSA-6790901; rRNA modification in the nucleus and cytosol.
DR SignaLink; Q9NXG2; -.
DR BioGRID-ORCS; 55623; 38 hits in 1076 CRISPR screens.
DR ChiTaRS; THUMPD1; human.
DR EvolutionaryTrace; Q9NXG2; -.
DR GenomeRNAi; 55623; -.
DR Pharos; Q9NXG2; Tdark.
DR PRO; PR:Q9NXG2; -.
DR Proteomes; UP000005640; Chromosome 16.
DR RNAct; Q9NXG2; protein.
DR Bgee; ENSG00000066654; Expressed in secondary oocyte and 212 other tissues.
DR ExpressionAtlas; Q9NXG2; baseline and differential.
DR Genevisible; Q9NXG2; HS.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0006400; P:tRNA modification; IBA:GO_Central.
DR CDD; cd11717; THUMP_THUMPD1_like; 1.
DR InterPro; IPR004114; THUMP_dom.
DR InterPro; IPR040183; THUMPD1-like.
DR PANTHER; PTHR13452; PTHR13452; 1.
DR Pfam; PF02926; THUMP; 1.
DR SMART; SM00981; THUMP; 1.
DR PROSITE; PS51165; THUMP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Phosphoprotein; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22814378"
FT CHAIN 2..353
FT /note="THUMP domain-containing protein 1"
FT /id="PRO_0000072530"
FT DOMAIN 147..254
FT /note="THUMP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00529"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 73..96
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 270..353
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 270..285
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 298..329
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22814378"
FT MOD_RES 79
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:24275569"
FT MOD_RES 86
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17081983,
FT ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163,
FT ECO:0007744|PubMed:24275569"
FT MOD_RES 88
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17081983,
FT ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163,
FT ECO:0007744|PubMed:24275569"
FT MOD_RES 119
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 270
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT VARIANT 236..353
FT /note="Missing (found in a patient with intellectual
FT disability, dysmorphic features, hypertension and diabetes;
FT unknown pathological significance)"
FT /evidence="ECO:0000269|PubMed:30237576"
FT /id="VAR_082156"
FT VARIANT 311
FT /note="E -> D (in dbSNP:rs11074471)"
FT /id="VAR_037645"
FT CONFLICT 84
FT /note="Q -> R (in Ref. 1; BAA91050)"
FT /evidence="ECO:0000305"
FT CONFLICT 285
FT /note="K -> E (in Ref. 1; BAA91050)"
FT /evidence="ECO:0000305"
FT CONFLICT 352
FT /note="F -> S (in Ref. 1; BAA91050)"
FT /evidence="ECO:0000305"
FT HELIX 171..188
FT /evidence="ECO:0007829|PDB:2DIR"
FT STRAND 195..201
FT /evidence="ECO:0007829|PDB:2DIR"
FT HELIX 210..224
FT /evidence="ECO:0007829|PDB:2DIR"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:2DIR"
FT STRAND 236..244
FT /evidence="ECO:0007829|PDB:2DIR"
FT STRAND 247..254
FT /evidence="ECO:0007829|PDB:2DIR"
SQ SEQUENCE 353 AA; 39315 MW; 7F0BBD91D204AA1B CRC64;
MAAPAQQTTQ PGGGKRKGKA QYVLAKRARR CDAGGPRQLE PGLQGILITC NMNERKCVEE
AYSLLNEYGD DMYGPEKFTD KDQQPSGSEG EDDDAEAALK KEVGDIKAST EMRLRRFQSV
ESGANNVVFI RTLGIEPEKL VHHILQDMYK TKKKKTRVIL RMLPISGTCK AFLEDMKKYA
ETFLEPWFKA PNKGTFQIVY KSRNNSHVNR EEVIRELAGI VCTLNSENKV DLTNPQYTVV
VEIIKAVCCL SVVKDYMLFR KYNLQEVVKS PKDPSQLNSK QGNGKEAKLE SADKSDQNNT
AEGKNNQQVP ENTEELGQTK PTSNPQVVNE GGAKPELASQ ATEGSKSNEN DFS
