GenomeNet

Database: UniProt
Entry: Q96EQ9
LinkDB: Q96EQ9
Original site: Q96EQ9 
ID   PRDM9_MOUSE             Reviewed;         843 AA.
AC   Q96EQ9; B8JJZ8; Q0D2N4;
DT   10-FEB-2009, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 2.
DT   13-FEB-2019, entry version 143.
DE   RecName: Full=Histone-lysine N-methyltransferase PRDM9;
DE            EC=2.1.1.43;
DE   AltName: Full=Hybrid sterility protein 1;
DE   AltName: Full=Meiosis-induced factor containing a PR/SET domain and zinc-finger motif;
DE   AltName: Full=PR domain zinc finger protein 9;
DE   AltName: Full=PR domain-containing protein 9;
GN   Name=Prdm9; Synonyms=Hst1, Meisetz;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
OC   Muroidea; Muridae; Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C57BL/6J;
RA   Brathwaite M., Waeltz P., Nagaraja R.;
RT   "Genomic sequence analysis in the mouse T-complex region.";
RL   Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C57BL/6J;
RX   PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA   Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
RA   She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
RA   Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
RA   Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
RA   Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
RA   Lindblad-Toh K., Eichler E.E., Ponting C.P.;
RT   "Lineage-specific biology revealed by a finished genome assembly of
RT   the mouse.";
RL   PLoS Biol. 7:E1000112-E1000112(2009).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
RC   TISSUE=Eye;
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
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY, ALTERNATIVE SPLICING (ISOFORMS 1; 2 AND
RP   3), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, AND
RP   MUTAGENESIS OF TYR-276 AND GLY-278.
RX   PubMed=16292313; DOI=10.1038/nature04112;
RA   Hayashi K., Yoshida K., Matsui Y.;
RT   "A histone H3 methyltransferase controls epigenetic events required
RT   for meiotic prophase.";
RL   Nature 438:374-378(2005).
RN   [5]
RP   IDENTIFICATION AS A SPECIATION GENE.
RX   PubMed=19074312; DOI=10.1126/science.1163601;
RA   Mihola O., Trachtulec Z., Vlcek C., Schimenti J.C., Forejt J.;
RT   "A mouse speciation gene encodes a meiotic histone H3
RT   methyltransferase.";
RL   Science 323:373-375(2009).
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       {ECO:0000269|PubMed:16292313}.
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         Evidence={ECO:0000269|PubMed:16292313};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}. Chromosome
CC       {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=4;
CC       Name=1; Synonyms=Meisetz;
CC         IsoId=Q96EQ9-1; Sequence=Displayed;
CC       Name=2; Synonyms=Meisetz-S1;
CC         IsoId=Q96EQ9-2; Sequence=VSP_036376, VSP_036377;
CC       Name=3; Synonyms=Meisetz-S2;
CC         IsoId=Q96EQ9-3; Sequence=VSP_036375, VSP_036378;
CC       Name=4;
CC         IsoId=Q96EQ9-4; Sequence=VSP_036374, VSP_036376, VSP_036377;
CC   -!- TISSUE SPECIFICITY: Specifically expressed in germ cells entering
CC       meiotic prophase in female fetal gonads and in postnatal testis.
CC       {ECO:0000269|PubMed:16292313}.
CC   -!- DEVELOPMENTAL STAGE: Specifically expressed during meiotic
CC       prophase. Transiently increases in female gonads from 13.5 dpc to
CC       16.5 dpc, the time during which meiosis proceeds from pre-meiotic
CC       replication to pachytene stages. Its expression is barely
CC       detectable in fetal male gonads. In adults, it is expressed in
CC       testis, but not in any other tissue tested. Abundance increases
CC       from 10 d post partum (dpp) to 18 dpp, during which time the first
CC       wave of spermatogenesis proceeds synchronously from pre-leptotene
CC       to pachytene stages. {ECO:0000269|PubMed:16292313}.
CC   -!- DISRUPTION PHENOTYPE: Sterility in both sexes due to severe
CC       impairment of the double-stranded break repair pathway, deficient
CC       pairing of homologous chromosomes and impaired sex body formation.
CC       In testis, H3 'Lys-4' trimethylation is attenuated and meiotic
CC       gene transcription is altered. {ECO:0000269|PubMed:16292313}.
CC   -!- MISCELLANEOUS: Represents a speciation gene in mus genus. Prdm9 is
CC       one of several genes responsible for hybrid sterility between
CC       M.musculus and house mouse. Hybrid sterility is defined as a
CC       situation where parental forms, each fertile inter se, produce
CC       infertile offspring. Intersubspecific hybrids of house mouse
CC       display spermatogenic failures that are due to variations in the
CC       Prdm9 gene.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding
CC       methyltransferase superfamily. {ECO:0000255|PROSITE-
CC       ProRule:PRU00190}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAH49903.1; Type=Erroneous initiation; Evidence={ECO:0000305};
DR   EMBL; AY294423; AAQ01511.1; -; Genomic_DNA.
DR   EMBL; AC154378; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CT033750; CAX15894.1; -; Genomic_DNA.
DR   EMBL; BC012016; AAH12016.1; -; mRNA.
DR   EMBL; BC049903; AAH49903.1; ALT_INIT; mRNA.
DR   CCDS; CCDS49963.1; -. [Q96EQ9-1]
DR   UniGene; Mm.215162; -.
DR   PDB; 4C1Q; X-ray; 2.30 A; A/B=198-368.
DR   PDBsum; 4C1Q; -.
DR   ProteinModelPortal; Q96EQ9; -.
DR   SMR; Q96EQ9; -.
DR   STRING; 10090.ENSMUSP00000131871; -.
DR   iPTMnet; Q96EQ9; -.
DR   PhosphoSitePlus; Q96EQ9; -.
DR   PaxDb; Q96EQ9; -.
DR   PRIDE; Q96EQ9; -.
DR   Ensembl; ENSMUST00000147532; ENSMUSP00000118454; ENSMUSG00000051977. [Q96EQ9-4]
DR   Ensembl; ENSMUST00000167994; ENSMUSP00000131871; ENSMUSG00000051977. [Q96EQ9-1]
DR   UCSC; uc008aos.1; mouse. [Q96EQ9-4]
DR   UCSC; uc029tan.1; mouse. [Q96EQ9-1]
DR   MGI; MGI:2384854; Prdm9.
DR   eggNOG; KOG1721; Eukaryota.
DR   eggNOG; COG5048; LUCA.
DR   GeneTree; ENSGT00940000158211; -.
DR   HOGENOM; HOG000234617; -.
DR   HOVERGEN; HBG108291; -.
DR   InParanoid; Q96EQ9; -.
DR   PhylomeDB; Q96EQ9; -.
DR   Reactome; R-MMU-212436; Generic Transcription Pathway.
DR   PRO; PR:Q96EQ9; -.
DR   Proteomes; UP000000589; Chromosome 17.
DR   Bgee; ENSMUSG00000051977; Expressed in 53 organ(s), highest expression level in colon.
DR   ExpressionAtlas; Q96EQ9; baseline and differential.
DR   Genevisible; Q96EQ9; MM.
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:0042800; F:histone methyltransferase activity (H3-K4 specific); IDA:MGI.
DR   GO; GO:0018024; F:histone-lysine N-methyltransferase activity; ISO:MGI.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0010844; F:recombination hotspot binding; IDA:MGI.
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; IDA:MGI.
DR   GO; GO:0044212; F:transcription regulatory region DNA binding; ISS:UniProtKB.
DR   GO; GO:0034968; P:histone lysine methylation; IMP:MGI.
DR   GO; GO:0016571; P:histone methylation; IDA:MGI.
DR   GO; GO:0006311; P:meiotic gene conversion; ISO:MGI.
DR   GO; GO:0016584; P:nucleosome positioning; ISS:UniProtKB.
DR   GO; GO:0060903; P:positive regulation of meiosis I; IMP:MGI.
DR   GO; GO:0010845; P:positive regulation of reciprocal meiotic recombination; IMP:MGI.
DR   GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:MGI.
DR   GO; GO:0007283; P:spermatogenesis; 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; 11.
DR   SMART; SM00349; KRAB; 1.
DR   SMART; SM00355; ZnF_C2H2; 13.
DR   SUPFAM; SSF109640; SSF109640; 1.
DR   SUPFAM; SSF57667; SSF57667; 6.
DR   PROSITE; PS50806; KRAB_RELATED; 1.
DR   PROSITE; PS50280; SET; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 12.
DR   PROSITE; PS50157; ZINC_FINGER_C2H2_2; 12.
PE   1: Evidence at protein level;
KW   3D-structure; Activator; Alternative splicing; Chromatin regulator;
KW   Chromosome; Complete proteome; Meiosis; Metal-binding;
KW   Methyltransferase; Nucleus; Reference proteome; Repeat;
KW   S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW   Transferase; Zinc; Zinc-finger.
FT   CHAIN         1    843       Histone-lysine N-methyltransferase PRDM9.
FT                                /FTId=PRO_0000363960.
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     513    531       C2H2-type 2; degenerate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00042}.
FT   ZN_FING     537    559       C2H2-type 3. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     565    587       C2H2-type 4. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     593    615       C2H2-type 5. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     621    643       C2H2-type 6. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     649    671       C2H2-type 7. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     677    699       C2H2-type 8. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     705    727       C2H2-type 9. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     733    755       C2H2-type 10. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     761    783       C2H2-type 11. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     789    811       C2H2-type 12. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     817    839       C2H2-type 13. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   VAR_SEQ       1    121       Missing (in isoform 4).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_036374.
FT   VAR_SEQ     382    418       ELRTEIHPCLLCSLAFSSQKFLTQHMEWNHRTEIFPG ->
FT                                DLFIIICKYTVAVFRHTRRGSQILLRMVVSHHVVAGI (in
FT                                isoform 3). {ECO:0000305}.
FT                                /FTId=VSP_036375.
FT   VAR_SEQ     382    404       ELRTEIHPCLLCSLAFSSQKFLT -> GGHYYDSLKKKEKR
FT                                EFSLRIFIF (in isoform 2 and isoform 4).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_036376.
FT   VAR_SEQ     405    843       Missing (in isoform 2 and isoform 4).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_036377.
FT   VAR_SEQ     419    843       Missing (in isoform 3). {ECO:0000305}.
FT                                /FTId=VSP_036378.
FT   MUTAGEN     276    276       Y->F: Abolishes enzyme methyltransferase.
FT                                {ECO:0000269|PubMed:16292313}.
FT   MUTAGEN     278    278       G->A: Abolishes enzyme methyltransferase.
FT                                {ECO:0000269|PubMed:16292313}.
FT   STRAND      203    205       {ECO:0000244|PDB:4C1Q}.
FT   TURN        206    209       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      210    214       {ECO:0000244|PDB:4C1Q}.
FT   TURN        217    219       {ECO:0000244|PDB:4C1Q}.
FT   HELIX       237    240       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      246    250       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      258    262       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      278    281       {ECO:0000244|PDB:4C1Q}.
FT   HELIX       286    288       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      289    296       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      298    300       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      302    306       {ECO:0000244|PDB:4C1Q}.
FT   TURN        310    312       {ECO:0000244|PDB:4C1Q}.
FT   HELIX       315    318       {ECO:0000244|PDB:4C1Q}.
FT   TURN        325    327       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      330    335       {ECO:0000244|PDB:4C1Q}.
FT   STRAND      338    345       {ECO:0000244|PDB:4C1Q}.
FT   HELIX       359    364       {ECO:0000244|PDB:4C1Q}.
SQ   SEQUENCE   843 AA;  97365 MW;  323DD4F00447D598 CRC64;
     MNTNKLEENS PEEDTGKFEW KPKVKDEFKD ISIYFSKEEW AEMGEWEKIR YRNVKRNYKM
     LISIGLRAPR PAFMCYQRQA MKPQINDSED SDEEWTPKQQ VSPPWVPFRV KHSKQQKESS
     RMPFSGESNV KEGSGIENLL NTSGSEHVQK PVSSLEEGNT SGQHSGKKLK LRKKNVEVKM
     YRLRERKGLA YEEVSEPQDD DYLYCEKCQN FFIDSCPNHG PPLFVKDSMV DRGHPNHSVL
     SLPPGLRISP SGIPEAGLGV WNEASDLPVG LHFGPYEGQI TEDEEAANSG YSWLITKGRN
     CYEYVDGQDE SQANWMRYVN CARDDEEQNL VAFQYHRKIF YRTCRVIRPG CELLVWYGDE
     YGQELGIKWG SKMKKGFTAG RELRTEIHPC LLCSLAFSSQ KFLTQHMEWN HRTEIFPGTS
     ARINPKPGDP CSDQLQEQHV DSQNKNDKAS NEVKRKSKPR QRISTTFPST LKEQMRSEES
     KRTVEELRTG QTTNTEDTVK SFIASEISSI ERQCGQYFSD KSNVNEHQKT HTGEKPYVCR
     ECGRGFTQNS HLIQHQRTHT GEKPYVCREC GRGFTQKSDL IKHQRTHTGE KPYVCRECGR
     GFTQKSDLIK HQRTHTGEKP YVCRECGRGF TQKSVLIKHQ RTHTGEKPYV CRECGRGFTQ
     KSVLIKHQRT HTGEKPYVCR ECGRGFTAKS VLIQHQRTHT GEKPYVCREC GRGFTAKSNL
     IQHQRTHTGE KPYVCRECGR GFTAKSVLIQ HQRTHTGEKP YVCRECGRGF TAKSVLIQHQ
     RTHTGEKPYV CRECGRGFTQ KSNLIKHQRT HTGEKPYVCR ECGWGFTQKS DLIQHQRTHT
     REK
//
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