PRD11_HUMAN
ID PRD11_HUMAN Reviewed; 511 AA.
AC Q9NQV5; Q8N9F1;
DT 08-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=PR domain-containing protein 11;
DE EC=2.1.1.-;
GN Name=PRDM11; Synonyms=PFM8;
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 [MRNA] (ISOFORM 1).
RA Yang X.-H., Huang S.;
RT "A family of novel PR-domain (PRDM) genes as candidate tumor suppressors.";
RL Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Brain;
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16554811; DOI=10.1038/nature04632;
RA Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K.,
RA Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T.,
RA Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G.,
RA Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C.,
RA Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A.,
RA Hattori M., Rogers J., Lander E.S., Sakaki Y.;
RT "Human chromosome 11 DNA sequence and analysis including novel gene
RT identification.";
RL Nature 440:497-500(2006).
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-63, AND IDENTIFICATION BY
RP 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 [5]
RP TISSUE SPECIFICITY, POLYMORPHISM, AND DEVELOPMENTAL STAGE.
RX PubMed=24929828; DOI=10.1038/ng.3011;
RA Loth D.W., Artigas M.S., Gharib S.A., Wain L.V., Franceschini N., Koch B.,
RA Pottinger T.D., Smith A.V., Duan Q., Oldmeadow C., Lee M.K., Strachan D.P.,
RA James A.L., Huffman J.E., Vitart V., Ramasamy A., Wareham N.J., Kaprio J.,
RA Wang X.Q., Trochet H., Kaehoenen M., Flexeder C., Albrecht E., Lopez L.M.,
RA de Jong K., Thyagarajan B., Alves A.C., Enroth S., Omenaas E., Joshi P.K.,
RA Fall T., Vinuela A., Launer L.J., Loehr L.R., Fornage M., Li G., Wilk J.B.,
RA Tang W., Manichaikul A., Lahousse L., Harris T.B., North K.E.,
RA Rudnicka A.R., Hui J., Gu X., Lumley T., Wright A.F., Hastie N.D.,
RA Campbell S., Kumar R., Pin I., Scott R.A., Pietilaeinen K.H., Surakka I.,
RA Liu Y., Holliday E.G., Schulz H., Heinrich J., Davies G., Vonk J.M.,
RA Wojczynski M., Pouta A., Johansson A., Wild S.H., Ingelsson E.,
RA Rivadeneira F., Voelzke H., Hysi P.G., Eiriksdottir G., Morrison A.C.,
RA Rotter J.I., Gao W., Postma D.S., White W.B., Rich S.S., Hofman A.,
RA Aspelund T., Couper D., Smith L.J., Psaty B.M., Lohman K., Burchard E.G.,
RA Uitterlinden A.G., Garcia M., Joubert B.R., McArdle W.L., Musk A.B.,
RA Hansel N., Heckbert S.R., Zgaga L., van Meurs J.B., Navarro P., Rudan I.,
RA Oh Y.M., Redline S., Jarvis D.L., Zhao J.H., Rantanen T., O'Connor G.T.,
RA Ripatti S., Scott R.J., Karrasch S., Grallert H., Gaddis N.C., Starr J.M.,
RA Wijmenga C., Minster R.L., Lederer D.J., Pekkanen J., Gyllensten U.,
RA Campbell H., Morris A.P., Glaeser S., Hammond C.J., Burkart K.M.,
RA Beilby J., Kritchevsky S.B., Gudnason V., Hancock D.B., Williams O.D.,
RA Polasek O., Zemunik T., Kolcic I., Petrini M.F., Wjst M., Kim W.J.,
RA Porteous D.J., Scotland G., Smith B.H., Viljanen A., Helioevaara M.,
RA Attia J.R., Sayers I., Hampel R., Gieger C., Deary I.J., Boezen H.M.,
RA Newman A., Jarvelin M.R., Wilson J.F., Lind L., Stricker B.H., Teumer A.,
RA Spector T.D., Melen E., Peters M.J., Lange L.A., Barr R.G., Bracke K.R.,
RA Verhamme F.M., Sung J., Hiemstra P.S., Cassano P.A., Sood A., Hayward C.,
RA Dupuis J., Hall I.P., Brusselle G.G., Tobin M.D., London S.J.;
RT "Genome-wide association analysis identifies six new loci associated with
RT forced vital capacity.";
RL Nat. Genet. 46:669-677(2014).
RN [6]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-214, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25218447; DOI=10.1038/nsmb.2890;
RA Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M.,
RA Vertegaal A.C.;
RT "Uncovering global SUMOylation signaling networks in a site-specific
RT manner.";
RL Nat. Struct. Mol. Biol. 21:927-936(2014).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND VARIANTS GLU-200
RP AND SER-285.
RX PubMed=25499759; DOI=10.1182/blood-2014-03-560805;
RA Fog C.K., Asmar F., Come C., Jensen K.T., Johansen J.V., Kheir T.B.,
RA Jacobsen L., Friis C., Louw A., Rosgaard L., Obro N.F., Marquart H.V.,
RA Anthonsen K., Braat A.K., van Lohuizen M., Ralfkiaer E., Gronbaek K.,
RA Lund A.H.;
RT "Loss of PRDM11 promotes MYC-driven lymphomagenesis.";
RL Blood 125:1272-1281(2015).
RN [8]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-88; LYS-155; LYS-172; LYS-200 AND
RP LYS-214, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 79-314.
RG Structural genomics consortium (SGC);
RT "Crystal structure of methyltransferase domain of human PR domain-
RT containing protein 11.";
RL Submitted (APR-2011) to the PDB data bank.
CC -!- FUNCTION: May be involved in transcription regulation.
CC {ECO:0000269|PubMed:25499759}.
CC -!- INTERACTION:
CC Q9NQV5; Q14192: FHL2; NbExp=3; IntAct=EBI-12941246, EBI-701903;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:25499759}. Cytoplasm
CC {ECO:0000269|PubMed:25499759}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9NQV5-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9NQV5-2; Sequence=VSP_039836;
CC -!- TISSUE SPECIFICITY: Highly expressed in lung, including bronchial
CC epithelial cells and airway smooth muscle cells, as well as in
CC peripheral blood mononuclear cells. In tonsils, expressed in B-cell
CC types, including naive B-cells, centroblasts, centrocytes and memory B-
CC cells (at protein level). In benign hyperplastic lymph nodes, expressed
CC in germinal center cells in both the dark and light zones, as well as
CC in scattered cells in the mantle zone and the interfollicular area (at
CC protein level). {ECO:0000269|PubMed:24929828,
CC ECO:0000269|PubMed:25499759}.
CC -!- DEVELOPMENTAL STAGE: Differential expressed during pseudoglandular and
CC canalicular stages of lung development. {ECO:0000269|PubMed:24929828}.
CC -!- POLYMORPHISM: A genome-wide association analysis shows PRDM11
CC association with forced vital capacity (FVC), a spirometric measure of
CC pulmonary function, that reflects lung volume and is used to diagnose
CC and monitor lung diseases. {ECO:0000269|PubMed:24929828}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
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DR EMBL; AF275818; AAF87244.1; -; mRNA.
DR EMBL; AK094792; BAC04425.1; -; mRNA.
DR EMBL; AC103681; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR CCDS; CCDS58130.1; -. [Q9NQV5-2]
DR CCDS; CCDS7912.1; -. [Q9NQV5-2]
DR RefSeq; NP_001243624.1; NM_001256695.1.
DR RefSeq; NP_001243625.1; NM_001256696.1. [Q9NQV5-2]
DR RefSeq; XP_011518533.1; XM_011520231.2.
DR PDB; 3RAY; X-ray; 1.73 A; A=79-314.
DR PDBsum; 3RAY; -.
DR AlphaFoldDB; Q9NQV5; -.
DR SMR; Q9NQV5; -.
DR BioGRID; 121299; 21.
DR IntAct; Q9NQV5; 11.
DR MINT; Q9NQV5; -.
DR STRING; 9606.ENSP00000480626; -.
DR iPTMnet; Q9NQV5; -.
DR PhosphoSitePlus; Q9NQV5; -.
DR BioMuta; PRDM11; -.
DR DMDM; 308153475; -.
DR EPD; Q9NQV5; -.
DR jPOST; Q9NQV5; -.
DR MassIVE; Q9NQV5; -.
DR MaxQB; Q9NQV5; -.
DR PaxDb; Q9NQV5; -.
DR PeptideAtlas; Q9NQV5; -.
DR PRIDE; Q9NQV5; -.
DR ProteomicsDB; 82190; -. [Q9NQV5-1]
DR ProteomicsDB; 82191; -. [Q9NQV5-2]
DR ABCD; Q9NQV5; 6 sequenced antibodies.
DR Antibodypedia; 26153; 147 antibodies from 26 providers.
DR DNASU; 56981; -.
DR Ensembl; ENST00000424263.6; ENSP00000394314.2; ENSG00000019485.14. [Q9NQV5-2]
DR Ensembl; ENST00000530656.5; ENSP00000435976.1; ENSG00000019485.14. [Q9NQV5-1]
DR GeneID; 56981; -.
DR KEGG; hsa:56981; -.
DR UCSC; uc031qaa.2; human. [Q9NQV5-1]
DR CTD; 56981; -.
DR DisGeNET; 56981; -.
DR GeneCards; PRDM11; -.
DR HGNC; HGNC:13996; PRDM11.
DR HPA; ENSG00000019485; Low tissue specificity.
DR MIM; 616347; gene.
DR neXtProt; NX_Q9NQV5; -.
DR OpenTargets; ENSG00000019485; -.
DR PharmGKB; PA33709; -.
DR VEuPathDB; HostDB:ENSG00000019485; -.
DR eggNOG; KOG2461; Eukaryota.
DR GeneTree; ENSGT00940000159837; -.
DR HOGENOM; CLU_593911_0_0_1; -.
DR InParanoid; Q9NQV5; -.
DR OrthoDB; 1318335at2759; -.
DR PhylomeDB; Q9NQV5; -.
DR TreeFam; TF316279; -.
DR PathwayCommons; Q9NQV5; -.
DR SignaLink; Q9NQV5; -.
DR BioGRID-ORCS; 56981; 14 hits in 1066 CRISPR screens.
DR ChiTaRS; PRDM11; human.
DR GenomeRNAi; 56981; -.
DR Pharos; Q9NQV5; Tbio.
DR PRO; PR:Q9NQV5; -.
DR Proteomes; UP000005640; Chromosome 11.
DR RNAct; Q9NQV5; protein.
DR Bgee; ENSG00000019485; Expressed in epithelial cell of pancreas and 151 other tissues.
DR ExpressionAtlas; Q9NQV5; baseline and differential.
DR Genevisible; Q9NQV5; HS.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; ISS:UniProtKB.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0030308; P:negative regulation of cell growth; IDA:UniProtKB.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:2000271; P:positive regulation of fibroblast apoptotic process; IDA:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0051726; P:regulation of cell cycle; IMP:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0043408; P:regulation of MAPK cascade; IMP:UniProtKB.
DR CDD; cd19195; PR-SET_PRDM11; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR044405; PRDM11_PR/SET.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Isopeptide bond;
KW Methyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW Transferase; Ubl conjugation.
FT CHAIN 1..511
FT /note="PR domain-containing protein 11"
FT /id="PRO_0000047768"
FT DOMAIN 149..260
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT REGION 389..438
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 63
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648"
FT CROSSLNK 88
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 155
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 172
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 200
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 214
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25218447,
FT ECO:0007744|PubMed:28112733"
FT VAR_SEQ 1..34
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_039836"
FT VARIANT 200
FT /note="K -> E (in a patient with diffuse large B-cell
FT lymphoma; unknown pathological significance;
FT dbSNP:rs111724149)"
FT /evidence="ECO:0000269|PubMed:25499759"
FT /id="VAR_073689"
FT VARIANT 285
FT /note="R -> S (in a patient with diffuse large B-cell
FT lymphoma; unknown pathological significance;
FT dbSNP:rs35090414)"
FT /evidence="ECO:0000269|PubMed:25499759"
FT /id="VAR_073690"
FT CONFLICT 48
FT /note="A -> V (in Ref. 2; BAC04425)"
FT /evidence="ECO:0000305"
FT CONFLICT 58..67
FT /note="KTEVCSPLRD -> NPS (in Ref. 1; AAF87244)"
FT /evidence="ECO:0000305"
FT CONFLICT 214
FT /note="K -> E (in Ref. 1; AAF87244)"
FT /evidence="ECO:0000305"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:3RAY"
FT TURN 111..114
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:3RAY"
FT TURN 122..124
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:3RAY"
FT HELIX 142..145
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 151..155
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:3RAY"
FT TURN 212..214
FT /evidence="ECO:0007829|PDB:3RAY"
FT HELIX 217..220
FT /evidence="ECO:0007829|PDB:3RAY"
FT TURN 227..229
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 232..237
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 240..247
FT /evidence="ECO:0007829|PDB:3RAY"
FT STRAND 256..259
FT /evidence="ECO:0007829|PDB:3RAY"
FT HELIX 261..267
FT /evidence="ECO:0007829|PDB:3RAY"
SQ SEQUENCE 511 AA; 57863 MW; 81DCAA502315EA5B CRC64;
MLKMAEPIAS LMIVECRACL RCSPLFLYQR EKDRMTENMK ECLAQTNAAV GDMVTVVKTE
VCSPLRDQEY GQPCSRRPDS SAMEVEPKKL KGKRDLIVPK SFQQVDFWFC ESCQEYFVDE
CPNHGPPVFV SDTPVPVGIP DRAALTIPQG MEVVKDTSGE SDVRCVNEVI PKGHIFGPYE
GQISTQDKSA GFFSWLIVDK NNRYKSIDGS DETKANWMRY VVISREEREQ NLLAFQHSER
IYFRACRDIR PGEWLRVWYS EDYMKRLHSM SQETIHRNLA RGEKRLQREK SEQVLDNPED
LRGPIHLSVL RQGKSPYKRG FDEGDVHPQA KKKKIDLIFK DVLEASLESA KVEAHQLALS
TSLVIRKVPK YQDDAYSQCA TTMTHGVQNI GQTQGEGDWK VPQGVSKEPG QLEDEEEEPS
SFKADSPAEA SLASDPHELP TTSFCPNCIR LKKKVRELQA ELDMLKSGKL PEPPVLPPQV
LELPEFSDPA GKLVWMRLLS EGRVRSGLCG G
