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Q96EQ9

- PRDM9_MOUSE

UniProt

Q96EQ9 - PRDM9_MOUSE

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Protein
Histone-lysine N-methyltransferase PRDM9
Gene
Prdm9, Hst1, Meisetz
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri388 – 41124C2H2-type 1
Add
BLAST
Zinc fingeri513 – 53119C2H2-type 2; degenerate
Add
BLAST
Zinc fingeri537 – 55923C2H2-type 3
Add
BLAST
Zinc fingeri565 – 58723C2H2-type 4
Add
BLAST
Zinc fingeri593 – 61523C2H2-type 5
Add
BLAST
Zinc fingeri621 – 64323C2H2-type 6
Add
BLAST
Zinc fingeri649 – 67123C2H2-type 7
Add
BLAST
Zinc fingeri677 – 69923C2H2-type 8
Add
BLAST
Zinc fingeri705 – 72723C2H2-type 9
Add
BLAST
Zinc fingeri733 – 75523C2H2-type 10
Add
BLAST
Zinc fingeri761 – 78323C2H2-type 11
Add
BLAST
Zinc fingeri789 – 81123C2H2-type 12
Add
BLAST
Zinc fingeri817 – 83923C2H2-type 13
Add
BLAST

GO - Molecular functioni

  1. histone methyltransferase activity (H3-K4 specific) Source: MGI
  2. metal ion binding Source: UniProtKB-KW
  3. recombination hotspot binding Source: MGI
  4. sequence-specific DNA binding Source: MGI
Complete GO annotation...

GO - Biological processi

  1. histone H3-K4 methylation Source: GOC
  2. histone lysine methylation Source: MGI
  3. histone methylation Source: MGI
  4. meiotic nuclear division Source: UniProtKB-KW
  5. positive regulation of meiosis I Source: MGI
  6. positive regulation of reciprocal meiotic recombination Source: MGI
  7. positive regulation of transcription from RNA polymerase II promoter Source: MGI
  8. spermatogenesis Source: MGI
  9. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Methyltransferase, Transferase

Keywords - Biological processi

Meiosis, Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiREACT_198629. Meiotic recombination.
REACT_209769. Meiotic recombination.
REACT_27235. Meiotic Recombination.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase PRDM9 (EC:2.1.1.43)
Alternative name(s):
Hybrid sterility protein 1
Meiosis-induced factor containing a PR/SET domain and zinc-finger motif
PR domain zinc finger protein 9
PR domain-containing protein 9
Gene namesi
Name:Prdm9
Synonyms:Hst1, Meisetz
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 17

Organism-specific databases

MGIiMGI:2384854. Prdm9.

Subcellular locationi

Nucleus Inferred. Chromosome Inferred

GO - Cellular componenti

  1. chromosome Source: UniProtKB-SubCell
  2. nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Disruption phenotypei

Sterility in both sexes due to severe impairment of the double-stranded break repair pathway, deficient pairing of homologous chromosomes and impaired sex body formation. In testis, H3 'Lys-4' trimethylation is attenuated and meiotic gene transcription is altered.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi276 – 2761Y → F: Abolishes enzyme methyltransferase. 1 Publication
Mutagenesisi278 – 2781G → A: Abolishes enzyme methyltransferase. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 843843Histone-lysine N-methyltransferase PRDM9
PRO_0000363960Add
BLAST

Proteomic databases

PRIDEiQ96EQ9.

PTM databases

PhosphoSiteiQ96EQ9.

Expressioni

Tissue specificityi

Specifically expressed in germ cells entering meiotic prophase in female fetal gonads and in postnatal testis.1 Publication

Developmental stagei

Specifically expressed during meiotic prophase. Transiently increases in female gonads from E13.5 to E16.5, the time during which meiosis proceeds from pre-meiotic replication to pachytene stages. Its expression is barely detectable in fetal male gonads. In adults, it is expressed in testis, but not in any other tissue tested. Abundance increases from 10 d post partum (dpp) to 18 dpp, during which time the first wave of spermatogenesis proceeds synchronously from pre-leptotene to pachytene stages.1 Publication

Gene expression databases

ArrayExpressiQ96EQ9.
BgeeiQ96EQ9.
GenevestigatoriQ96EQ9.

Interactioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000040727.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi203 – 2053
Turni206 – 2094
Beta strandi210 – 2145
Turni217 – 2193
Helixi237 – 2404
Beta strandi246 – 2505
Beta strandi258 – 2625
Beta strandi278 – 2814
Helixi286 – 2883
Beta strandi289 – 2968
Beta strandi298 – 3003
Beta strandi302 – 3065
Turni310 – 3123
Helixi315 – 3184
Turni325 – 3273
Beta strandi330 – 3356
Beta strandi338 – 3458
Helixi359 – 3646

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C1QX-ray2.30A/B198-368[»]
ProteinModelPortaliQ96EQ9.
SMRiQ96EQ9. Positions 195-411, 489-843.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini23 – 8664KRAB-related
Add
BLAST
Domaini244 – 358115SET
Add
BLAST

Sequence similaritiesi

Contains 13 C2H2-type zinc fingers.
Contains 1 SET domain.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG241438.
GeneTreeiENSGT00530000063157.
HOGENOMiHOG000234617.
HOVERGENiHBG108291.
PhylomeDBiQ96EQ9.

Family and domain databases

Gene3Di3.30.160.60. 12 hits.
InterProiIPR001909. Krueppel-associated_box.
IPR003655. Krueppel-associated_box-rel.
IPR001214. SET_dom.
IPR019041. SSXRD_motif.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 13 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 12 hits.
PS50157. ZINC_FINGER_C2H2_2. 12 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q96EQ9-1) [UniParc]FASTAAdd to Basket

Also known as: Meisetz

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

MNTNKLEENS PEEDTGKFEW KPKVKDEFKD ISIYFSKEEW AEMGEWEKIR    50
YRNVKRNYKM LISIGLRAPR PAFMCYQRQA MKPQINDSED SDEEWTPKQQ 100
VSPPWVPFRV KHSKQQKESS RMPFSGESNV KEGSGIENLL NTSGSEHVQK 150
PVSSLEEGNT SGQHSGKKLK LRKKNVEVKM YRLRERKGLA YEEVSEPQDD 200
DYLYCEKCQN FFIDSCPNHG PPLFVKDSMV DRGHPNHSVL SLPPGLRISP 250
SGIPEAGLGV WNEASDLPVG LHFGPYEGQI TEDEEAANSG YSWLITKGRN 300
CYEYVDGQDE SQANWMRYVN CARDDEEQNL VAFQYHRKIF YRTCRVIRPG 350
CELLVWYGDE YGQELGIKWG SKMKKGFTAG RELRTEIHPC LLCSLAFSSQ 400
KFLTQHMEWN HRTEIFPGTS ARINPKPGDP CSDQLQEQHV DSQNKNDKAS 450
NEVKRKSKPR QRISTTFPST LKEQMRSEES KRTVEELRTG QTTNTEDTVK 500
SFIASEISSI ERQCGQYFSD KSNVNEHQKT HTGEKPYVCR ECGRGFTQNS 550
HLIQHQRTHT GEKPYVCREC GRGFTQKSDL IKHQRTHTGE KPYVCRECGR 600
GFTQKSDLIK HQRTHTGEKP YVCRECGRGF TQKSVLIKHQ RTHTGEKPYV 650
CRECGRGFTQ KSVLIKHQRT HTGEKPYVCR ECGRGFTAKS VLIQHQRTHT 700
GEKPYVCREC GRGFTAKSNL IQHQRTHTGE KPYVCRECGR GFTAKSVLIQ 750
HQRTHTGEKP YVCRECGRGF TAKSVLIQHQ RTHTGEKPYV CRECGRGFTQ 800
KSNLIKHQRT HTGEKPYVCR ECGWGFTQKS DLIQHQRTHT REK 843
Length:843
Mass (Da):97,365
Last modified:February 10, 2009 - v2
Checksum:i323DD4F00447D598
GO
Isoform 2 (identifier: Q96EQ9-2) [UniParc]FASTAAdd to Basket

Also known as: Meisetz-S1

The sequence of this isoform differs from the canonical sequence as follows:
     382-404: ELRTEIHPCLLCSLAFSSQKFLT → GGHYYDSLKKKEKREFSLRIFIF
     405-843: Missing.

Show »
Length:404
Mass (Da):46,856
Checksum:iE8D64C40EFB5EC84
GO
Isoform 3 (identifier: Q96EQ9-3) [UniParc]FASTAAdd to Basket

Also known as: Meisetz-S2

The sequence of this isoform differs from the canonical sequence as follows:
     382-418: ELRTEIHPCLLCSLAFSSQKFLTQHMEWNHRTEIFPG → DLFIIICKYTVAVFRHTRRGSQILLRMVVSHHVVAGI
     419-843: Missing.

Show »
Length:418
Mass (Da):48,244
Checksum:i0EBDF88F535CEE94
GO
Isoform 4 (identifier: Q96EQ9-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-121: Missing.
     382-404: ELRTEIHPCLLCSLAFSSQKFLT → GGHYYDSLKKKEKREFSLRIFIF
     405-843: Missing.

Show »
Length:283
Mass (Da):32,241
Checksum:iF4FE5CE36B04C03E
GO

Sequence cautioni

The sequence AAH49903.1 differs from that shown. Reason: Erroneous initiation.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 121121Missing in isoform 4.
VSP_036374Add
BLAST
Alternative sequencei382 – 41837ELRTE…EIFPG → DLFIIICKYTVAVFRHTRRG SQILLRMVVSHHVVAGI in isoform 3.
VSP_036375Add
BLAST
Alternative sequencei382 – 40423ELRTE…QKFLT → GGHYYDSLKKKEKREFSLRI FIF in isoform 2 and isoform 4.
VSP_036376Add
BLAST
Alternative sequencei405 – 843439Missing in isoform 2 and isoform 4.
VSP_036377Add
BLAST
Alternative sequencei419 – 843425Missing in isoform 3.
VSP_036378Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY294423 Genomic DNA. Translation: AAQ01511.1.
AC154378 Genomic DNA. No translation available.
CT033750 Genomic DNA. Translation: CAX15894.1.
BC012016 mRNA. Translation: AAH12016.1.
BC049903 mRNA. Translation: AAH49903.1. Different initiation.
UniGeneiMm.215162.

Genome annotation databases

EnsembliENSMUST00000147532; ENSMUSP00000118454; ENSMUSG00000051977. [Q96EQ9-4]
UCSCiuc008aos.1. mouse. [Q96EQ9-4]
uc029tan.1. mouse. [Q96EQ9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY294423 Genomic DNA. Translation: AAQ01511.1 .
AC154378 Genomic DNA. No translation available.
CT033750 Genomic DNA. Translation: CAX15894.1 .
BC012016 mRNA. Translation: AAH12016.1 .
BC049903 mRNA. Translation: AAH49903.1 . Different initiation.
UniGenei Mm.215162.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4C1Q X-ray 2.30 A/B 198-368 [» ]
ProteinModelPortali Q96EQ9.
SMRi Q96EQ9. Positions 195-411, 489-843.
ModBasei Search...

Protein-protein interaction databases

STRINGi 10090.ENSMUSP00000040727.

PTM databases

PhosphoSitei Q96EQ9.

Proteomic databases

PRIDEi Q96EQ9.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000147532 ; ENSMUSP00000118454 ; ENSMUSG00000051977 . [Q96EQ9-4 ]
UCSCi uc008aos.1. mouse. [Q96EQ9-4 ]
uc029tan.1. mouse. [Q96EQ9-1 ]

Organism-specific databases

MGIi MGI:2384854. Prdm9.

Phylogenomic databases

eggNOGi NOG241438.
GeneTreei ENSGT00530000063157.
HOGENOMi HOG000234617.
HOVERGENi HBG108291.
PhylomeDBi Q96EQ9.

Enzyme and pathway databases

Reactomei REACT_198629. Meiotic recombination.
REACT_209769. Meiotic recombination.
REACT_27235. Meiotic Recombination.

Miscellaneous databases

NextBioi 13887360.
PROi Q96EQ9.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q96EQ9.
Bgeei Q96EQ9.
Genevestigatori Q96EQ9.

Family and domain databases

Gene3Di 3.30.160.60. 12 hits.
InterProi IPR001909. Krueppel-associated_box.
IPR003655. Krueppel-associated_box-rel.
IPR001214. SET_dom.
IPR019041. SSXRD_motif.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view ]
Pfami PF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
[Graphical view ]
SMARTi SM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 13 hits.
[Graphical view ]
SUPFAMi SSF109640. SSF109640. 1 hit.
PROSITEi PS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 12 hits.
PS50157. ZINC_FINGER_C2H2_2. 12 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Genomic sequence analysis in the mouse T-complex region."
    Brathwaite M., Waeltz P., Nagaraja R.
    Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
    Tissue: Eye.
  4. "A histone H3 methyltransferase controls epigenetic events required for meiotic prophase."
    Hayashi K., Yoshida K., Matsui Y.
    Nature 438:374-378(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, ALTERNATIVE SPLICING (ISOFORMS 1; 2 AND 3), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, MUTAGENESIS OF TYR-276 AND GLY-278.
  5. "A mouse speciation gene encodes a meiotic histone H3 methyltransferase."
    Mihola O., Trachtulec Z., Vlcek C., Schimenti J.C., Forejt J.
    Science 323:373-375(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION AS A SPECIATION GENE.

Entry informationi

Entry nameiPRDM9_MOUSE
AccessioniPrimary (citable) accession number: Q96EQ9
Secondary accession number(s): B8JJZ8, Q0D2N4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: February 10, 2009
Last modified: September 3, 2014
This is version 106 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Represents a speciation gene in mus genus. Prdm9 is one of several genes responsible for hybrid sterility between M.musculus and house mouse. Hybrid sterility is defined as a situation where parental forms, each fertile inter se, produce infertile offspring. Intersubspecific hybrids of house mouse display spermatogenic failures that are due to variations in the Prdm9 gene.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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