GenomeNet

Database: UniProt
Entry: Q9NQV7
LinkDB: Q9NQV7
Original site: Q9NQV7 
ID   PRDM9_HUMAN             Reviewed;         894 AA.
AC   Q9NQV7; B4DX22; Q27Q50;
DT   16-NOV-2001, integrated into UniProtKB/Swiss-Prot.
DT   04-NOV-2008, sequence version 2.
DT   13-FEB-2019, entry version 157.
DE   RecName: Full=Histone-lysine N-methyltransferase PRDM9;
DE            EC=2.1.1.43;
DE   AltName: Full=PR domain zinc finger protein 9;
DE   AltName: Full=PR domain-containing protein 9;
GN   Name=PRDM9; Synonyms=PFM6;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Ying J., Wong A.H.Y., Li H., Wang Y., Tao Q.;
RT   "Cloning and characterization of PR domain-containing 9 (PRDM9).";
RL   Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Testis;
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.,
RA   Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA   Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA   Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA   Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA   Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA   Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA   Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA   Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA   Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA   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.,
RA   Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA   Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA   Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA   Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA   Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA   Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA   Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA   Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA   Nakai K., Yada T., Nakamura Y., Ohara O., 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=15372022; DOI=10.1038/nature02919;
RA   Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S.,
RA   Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M.,
RA   She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.,
RA   Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M.,
RA   Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T.,
RA   Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M.,
RA   Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K.,
RA   Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C.,
RA   Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M.,
RA   Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A.,
RA   Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M.,
RA   Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M.,
RA   Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S.,
RA   Richardson P., Lucas S.M., Myers R.M., Rubin E.M.;
RT   "The DNA sequence and comparative analysis of human chromosome 5.";
RL   Nature 431:268-274(2004).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 205-894.
RX   PubMed=10668202;
RA   Jiang G.L., Huang S.;
RT   "The yin-yang of PR-domain family genes in tumorigenesis.";
RL   Histol. Histopathol. 15:109-117(2000).
RN   [5]
RP   VARIANT HIS-335.
RX   PubMed=18941885; DOI=10.1007/s10815-008-9270-x;
RA   Miyamoto T., Koh E., Sakugawa N., Sato H., Hayashi H., Namiki M.,
RA   Sengoku K.;
RT   "Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a
RT   genetic risk factor for Japanese patients with azoospermia by meiotic
RT   arrest.";
RL   J. Assist. Reprod. Genet. 25:553-557(2008).
CC   -!- FUNCTION: Histone methyltransferase that specifically
CC       trimethylates 'Lys-4' of histone H3 during meiotic prophase and is
CC       essential for proper meiotic progression. Does not have the
CC       ability to mono- and dimethylate 'Lys-4' of histone H3. H3 'Lys-4'
CC       methylation represents a specific tag for epigenetic
CC       transcriptional activation. Plays a central role in the
CC       transcriptional activation of genes during early meiotic prophase
CC       (By similarity). {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) +
CC         N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC         ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.43;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome
CC       {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding
CC       methyltransferase superfamily. {ECO:0000255|PROSITE-
CC       ProRule:PRU00190}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAF87242.1; Type=Erroneous initiation; Evidence={ECO:0000305};
DR   EMBL; DQ388610; ABD47939.1; -; mRNA.
DR   EMBL; AK301776; BAG63234.1; -; mRNA.
DR   EMBL; AC025451; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AF275816; AAF87242.1; ALT_INIT; mRNA.
DR   CCDS; CCDS43307.1; -.
DR   RefSeq; NP_001297143.1; NM_001310214.1.
DR   RefSeq; NP_064612.2; NM_020227.3.
DR   UniGene; Hs.283096; -.
DR   PDB; 4IJD; X-ray; 2.15 A; A/B=195-415.
DR   PDB; 5EGB; X-ray; 1.98 A; A=717-858.
DR   PDB; 5EH2; X-ray; 2.05 A; E/F=717-858.
DR   PDB; 5EI9; X-ray; 1.92 A; E/F=717-858.
DR   PDBsum; 4IJD; -.
DR   PDBsum; 5EGB; -.
DR   PDBsum; 5EH2; -.
DR   PDBsum; 5EI9; -.
DR   ProteinModelPortal; Q9NQV7; -.
DR   SMR; Q9NQV7; -.
DR   IntAct; Q9NQV7; 6.
DR   STRING; 9606.ENSP00000296682; -.
DR   ChEMBL; CHEMBL3588737; -.
DR   iPTMnet; Q9NQV7; -.
DR   PhosphoSitePlus; Q9NQV7; -.
DR   BioMuta; PRDM9; -.
DR   DMDM; 212276459; -.
DR   PaxDb; Q9NQV7; -.
DR   PeptideAtlas; Q9NQV7; -.
DR   PRIDE; Q9NQV7; -.
DR   ProteomicsDB; 82198; -.
DR   Ensembl; ENST00000296682; ENSP00000296682; ENSG00000164256.
DR   GeneID; 56979; -.
DR   KEGG; hsa:56979; -.
DR   UCSC; uc003jgo.3; human.
DR   CTD; 56979; -.
DR   DisGeNET; 56979; -.
DR   EuPathDB; HostDB:ENSG00000164256.10; -.
DR   GeneCards; PRDM9; -.
DR   HGNC; HGNC:13994; PRDM9.
DR   HPA; HPA059555; -.
DR   MIM; 609760; gene.
DR   neXtProt; NX_Q9NQV7; -.
DR   OpenTargets; ENSG00000164256; -.
DR   PharmGKB; PA33721; -.
DR   eggNOG; KOG1721; Eukaryota.
DR   eggNOG; COG5048; LUCA.
DR   GeneTree; ENSGT00940000163405; -.
DR   HOGENOM; HOG000234617; -.
DR   HOVERGEN; HBG108291; -.
DR   InParanoid; Q9NQV7; -.
DR   KO; K20796; -.
DR   OMA; PSVCREC; -.
DR   OrthoDB; 1318335at2759; -.
DR   PhylomeDB; Q9NQV7; -.
DR   TreeFam; TF338096; -.
DR   Reactome; R-HSA-3214841; PKMTs methylate histone lysines.
DR   Reactome; R-HSA-912446; Meiotic recombination.
DR   GeneWiki; PRDM9; -.
DR   GenomeRNAi; 56979; -.
DR   PRO; PR:Q9NQV7; -.
DR   Proteomes; UP000005640; Chromosome 5.
DR   Bgee; ENSG00000164256; Expressed in 38 organ(s), highest expression level in testis.
DR   ExpressionAtlas; Q9NQV7; baseline and differential.
DR   Genevisible; Q9NQV7; HS.
DR   GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR   GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; IBA:GO_Central.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; ISA:NTNU_SB.
DR   GO; GO:0042800; F:histone methyltransferase activity (H3-K4 specific); IBA:GO_Central.
DR   GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IMP:UniProtKB.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0010844; F:recombination hotspot binding; IMP:UniProtKB.
DR   GO; GO:0000977; F:RNA polymerase II regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0043565; F:sequence-specific DNA binding; IMP:UniProtKB.
DR   GO; GO:0044212; F:transcription regulatory region DNA binding; IMP:UniProtKB.
DR   GO; GO:0006311; P:meiotic gene conversion; IDA:MGI.
DR   GO; GO:0016584; P:nucleosome positioning; IMP:UniProtKB.
DR   GO; GO:0010845; P:positive regulation of reciprocal meiotic recombination; IMP:MGI.
DR   CDD; cd07765; KRAB_A-box; 1.
DR   InterPro; IPR001909; KRAB.
DR   InterPro; IPR036051; KRAB_dom_sf.
DR   InterPro; IPR003655; Krueppel-associated_box-rel.
DR   InterPro; IPR001214; SET_dom.
DR   InterPro; IPR019041; SSXRD_motif.
DR   InterPro; IPR036236; Znf_C2H2_sf.
DR   InterPro; IPR013087; Znf_C2H2_type.
DR   Pfam; PF01352; KRAB; 1.
DR   Pfam; PF00856; SET; 1.
DR   Pfam; PF09514; SSXRD; 1.
DR   Pfam; PF00096; zf-C2H2; 9.
DR   SMART; SM00349; KRAB; 1.
DR   SMART; SM00355; ZnF_C2H2; 14.
DR   SUPFAM; SSF109640; SSF109640; 1.
DR   SUPFAM; SSF57667; SSF57667; 7.
DR   PROSITE; PS50806; KRAB_RELATED; 1.
DR   PROSITE; PS50280; SET; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 13.
DR   PROSITE; PS50157; ZINC_FINGER_C2H2_2; 14.
PE   1: Evidence at protein level;
KW   3D-structure; Activator; Chromatin regulator; Chromosome;
KW   Complete proteome; Meiosis; Metal-binding; Methyltransferase; Nucleus;
KW   Polymorphism; Reference proteome; Repeat; S-adenosyl-L-methionine;
KW   Transcription; Transcription regulation; Transferase; Zinc;
KW   Zinc-finger.
FT   CHAIN         1    894       Histone-lysine N-methyltransferase PRDM9.
FT                                /FTId=PRO_0000047766.
FT   DOMAIN       23     86       KRAB-related. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00120}.
FT   DOMAIN      244    358       SET. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00190}.
FT   ZN_FING     388    411       C2H2-type 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     524    546       C2H2-type 2; degenerate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00042}.
FT   ZN_FING     552    574       C2H2-type 3. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     580    602       C2H2-type 4. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     608    630       C2H2-type 5. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     636    658       C2H2-type 6. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     664    686       C2H2-type 7. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     692    714       C2H2-type 8. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     720    742       C2H2-type 9. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     748    770       C2H2-type 10. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     776    798       C2H2-type 11. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     804    826       C2H2-type 12. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     832    854       C2H2-type 13. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     860    882       C2H2-type 14. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   VARIANT     335    335       Y -> H (common polymorphism; may be a
FT                                genetic risk for patients with
FT                                azoospermia caused by meiotic arrest).
FT                                {ECO:0000269|PubMed:18941885}.
FT                                /FTId=VAR_054417.
FT   CONFLICT    295    295       I -> VRRACHF (in Ref. 4; AAF87242).
FT                                {ECO:0000305}.
FT   CONFLICT    377    381       Missing (in Ref. 4; AAF87242).
FT                                {ECO:0000305}.
FT   CONFLICT    681    681       T -> S (in Ref. 2; BAG63234).
FT                                {ECO:0000305}.
FT   HELIX       199    201       {ECO:0000244|PDB:4IJD}.
FT   STRAND      203    205       {ECO:0000244|PDB:4IJD}.
FT   TURN        206    209       {ECO:0000244|PDB:4IJD}.
FT   STRAND      210    216       {ECO:0000244|PDB:4IJD}.
FT   TURN        217    219       {ECO:0000244|PDB:4IJD}.
FT   HELIX       237    240       {ECO:0000244|PDB:4IJD}.
FT   STRAND      246    250       {ECO:0000244|PDB:4IJD}.
FT   STRAND      258    262       {ECO:0000244|PDB:4IJD}.
FT   STRAND      278    281       {ECO:0000244|PDB:4IJD}.
FT   HELIX       284    286       {ECO:0000244|PDB:4IJD}.
FT   STRAND      289    298       {ECO:0000244|PDB:4IJD}.
FT   STRAND      301    306       {ECO:0000244|PDB:4IJD}.
FT   TURN        310    312       {ECO:0000244|PDB:4IJD}.
FT   HELIX       315    318       {ECO:0000244|PDB:4IJD}.
FT   TURN        325    327       {ECO:0000244|PDB:4IJD}.
FT   STRAND      330    335       {ECO:0000244|PDB:4IJD}.
FT   STRAND      338    345       {ECO:0000244|PDB:4IJD}.
FT   STRAND      354    356       {ECO:0000244|PDB:4IJD}.
FT   HELIX       362    367       {ECO:0000244|PDB:4IJD}.
FT   TURN        368    370       {ECO:0000244|PDB:4IJD}.
FT   HELIX       373    377       {ECO:0000244|PDB:4IJD}.
FT   STRAND      391    394       {ECO:0000244|PDB:4IJD}.
FT   STRAND      396    399       {ECO:0000244|PDB:4IJD}.
FT   HELIX       400    410       {ECO:0000244|PDB:4IJD}.
FT   TURN        723    725       {ECO:0000244|PDB:5EI9}.
FT   STRAND      728    731       {ECO:0000244|PDB:5EI9}.
FT   HELIX       732    743       {ECO:0000244|PDB:5EI9}.
FT   TURN        751    753       {ECO:0000244|PDB:5EI9}.
FT   STRAND      756    759       {ECO:0000244|PDB:5EI9}.
FT   HELIX       760    765       {ECO:0000244|PDB:5EI9}.
FT   HELIX       768    771       {ECO:0000244|PDB:5EI9}.
FT   TURN        779    781       {ECO:0000244|PDB:5EI9}.
FT   STRAND      784    787       {ECO:0000244|PDB:5EI9}.
FT   HELIX       788    799       {ECO:0000244|PDB:5EI9}.
FT   TURN        807    809       {ECO:0000244|PDB:5EI9}.
FT   STRAND      812    815       {ECO:0000244|PDB:5EI9}.
FT   HELIX       816    823       {ECO:0000244|PDB:5EI9}.
FT   TURN        824    826       {ECO:0000244|PDB:5EI9}.
SQ   SEQUENCE   894 AA;  103376 MW;  DE53094C32EFF83B CRC64;
     MSPEKSQEES PEEDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR YRNVKRNYNA
     LITIGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ VKPPWMALRV EQRKHQKGMP
     KASFSNESSL KELSRTANLL NASGSEQAQK PVSPSGEAST SGQHSRLKLE LRKKETERKM
     YSLRERKGHA YKEVSEPQDD DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL
     SLPPGLRIGP SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANNG YSWLITKGRN
     CYEYVDGKDK SWANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG CELLVWYGDE
     YGQELGIKWG SKWKKELMAG REPKPEIHPC PSCCLAFSSQ KFLSQHVERN HSSQNFPGPS
     ARKLLQPENP CPGDQNQEQQ YPDPHSRNDK TKGQEIKERS KLLNKRTWQR EISRAFSSPP
     KGQMGSCRVG KRIMEEESRT GQKVNPGNTG KLFVGVGISR IAKVKYGECG QGFSVKSDVI
     THQRTHTGEK LYVCRECGRG FSWKSHLLIH QRIHTGEKPY VCRECGRGFS WQSVLLTHQR
     THTGEKPYVC RECGRGFSRQ SVLLTHQRRH TGEKPYVCRE CGRGFSRQSV LLTHQRRHTG
     EKPYVCRECG RGFSWQSVLL THQRTHTGEK PYVCRECGRG FSWQSVLLTH QRTHTGEKPY
     VCRECGRGFS NKSHLLRHQR THTGEKPYVC RECGRGFRDK SHLLRHQRTH TGEKPYVCRE
     CGRGFRDKSN LLSHQRTHTG EKPYVCRECG RGFSNKSHLL RHQRTHTGEK PYVCRECGRG
     FRNKSHLLRH QRTHTGEKPY VCRECGRGFS DRSSLCYHQR THTGEKPYVC REDE
//
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