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Protein

Histone-lysine N-methyltransferase PRDM9

Gene

Prdm9

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 (By similarity).By similarity

Catalytic activityi

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri392 – 41524C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri522 – 54019C2H2-type 2; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri546 – 56823C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri574 – 59623C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri602 – 62423C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri630 – 65223C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri658 – 68023C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri686 – 70823C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri714 – 73623C2H2-type 9PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri742 – 76423C2H2-type 10PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri770 – 79223C2H2-type 11PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase PRDM9 (EC:2.1.1.43)
Alternative name(s):
PR domain zinc finger protein 9
PR domain-containing protein 9
Gene namesi
Name:Prdm9
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 1

Organism-specific databases

RGDi1305247. Prdm9.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 796796Histone-lysine N-methyltransferase PRDM9PRO_0000363961Add
BLAST

Proteomic databases

PaxDbiP0C6Y7.
PRIDEiP0C6Y7.

Interactioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000060531.

Structurei

3D structure databases

ProteinModelPortaliP0C6Y7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini27 – 9064KRAB-relatedPROSITE-ProRule annotationAdd
BLAST
Domaini248 – 362115SETPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 11 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 KRAB-related domain.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri392 – 41524C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri522 – 54019C2H2-type 2; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri546 – 56823C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri574 – 59623C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri602 – 62423C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri630 – 65223C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri658 – 68023C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri686 – 70823C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri714 – 73623C2H2-type 9PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri742 – 76423C2H2-type 10PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri770 – 79223C2H2-type 11PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
KOG2461. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000234617.
HOVERGENiHBG108291.
InParanoidiP0C6Y7.
OMAiRSCNDKT.
OrthoDBiEOG7KSX7Q.
PhylomeDBiP0C6Y7.
TreeFamiTF338096.

Family and domain databases

Gene3Di3.30.160.60. 10 hits.
InterProiIPR001909. KRAB.
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.
PF00856. SET. 1 hit.
PF09514. SSXRD. 1 hit.
PF00096. zf-C2H2. 7 hits.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 11 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 10 hits.
PS50157. ZINC_FINGER_C2H2_2. 10 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P0C6Y7-1) [UniParc]FASTAAdd to basket

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

        10         20         30         40         50
MSRTMNTNKP EENSTEGDAG KLEWKPKVKD EFKDISIYFS KEEWAEMGEW
60 70 80 90 100
EKIRYRNVKR NYKMLISIGL RAPRPAFMCY QRQAIKPQIN DNEDSDEEWT
110 120 130 140 150
PKQQVSSPWV PFRVKHSKQQ KETPRMPLSD KSSVKEVFGI ENLLNTSGSE
160 170 180 190 200
HAQKPVCSPE EGNTSGQHFG KKLKLRRKNV EVNRYRLRER KDLAYEEVSE
210 220 230 240 250
PQDDDYLYCE KCQNFFIDSC PNHGPPVFVK DSVVDRGHPN HSVLSLPPGL
260 270 280 290 300
RIGPSGIPEA GLGVWNEASD LPVGLHFGPY KGQITEDEEA ANSGYSWLIT
310 320 330 340 350
KGRNCYEYVD GQDESQANWM RYVNCARDDE EQNLVAFQYH RKIFYRTCRV
360 370 380 390 400
IRPGRELLVW YGDEYGQELG IKWGSKMKKG FTAGRELRTE IHPCFLCSLA
410 420 430 440 450
FSSQKFLTQH VEWNHRTEIF PGASARINPK PGDPCPDQLQ EHFDSQNKND
460 470 480 490 500
KASNEVKRKS KPRHKWTRQR ISTAFSSTLK EQMRSEESKR TVEEELRTGQ
510 520 530 540 550
TTNIEDTAKS FIASETSRIE RQCGQCFSDK SNVSEHQRTH TGEKPYICRE
560 570 580 590 600
CGRGFSQKSD LIKHQRTHTE EKPYICRECG RGFTQKSDLI KHQRTHTEEK
610 620 630 640 650
PYICRECGRG FTQKSDLIKH QRTHTGEKPY ICRECGRGFT QKSDLIKHQR
660 670 680 690 700
THTEEKPYIC RECGRGFTQK SSLIRHQRTH TGEKPYICRE CGLGFTQKSN
710 720 730 740 750
LIRHLRTHTG EKPYICRECG LGFTRKSNLI QHQRTHTGEK PYICRECGQG
760 770 780 790
LTWKSSLIQH QRTHTGEKPY ICRECGRGFT WKSSLIQHQR THTVEK
Length:796
Mass (Da):92,579
Last modified:February 10, 2009 - v1
Checksum:i7FB5104B805F87D9
GO
Isoform 2 (identifier: P0C6Y7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-125: Missing.
     386-408: ELRTEIHPCFLCSLAFSSQKFLT → GGYHYDSLKEKEKMDFSLRIFIF
     409-796: Missing.

Show »
Length:283
Mass (Da):32,406
Checksum:iAE2D191116075BA2
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 125125Missing in isoform 2. CuratedVSP_036379Add
BLAST
Alternative sequencei386 – 40823ELRTE…QKFLT → GGYHYDSLKEKEKMDFSLRI FIF in isoform 2. CuratedVSP_036380Add
BLAST
Alternative sequencei409 – 796388Missing in isoform 2. CuratedVSP_036381Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CH474033 Genomic DNA. Translation: EDL99813.1.
RefSeqiNP_001102373.2. NM_001108903.2. [P0C6Y7-1]
UniGeneiRn.124847.

Genome annotation databases

EnsembliENSRNOT00000066370; ENSRNOP00000060531; ENSRNOG00000021493. [P0C6Y7-1]
GeneIDi365155.
KEGGirno:365155.
UCSCiRGD:1305247. rat. [P0C6Y7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CH474033 Genomic DNA. Translation: EDL99813.1.
RefSeqiNP_001102373.2. NM_001108903.2. [P0C6Y7-1]
UniGeneiRn.124847.

3D structure databases

ProteinModelPortaliP0C6Y7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000060531.

Proteomic databases

PaxDbiP0C6Y7.
PRIDEiP0C6Y7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000066370; ENSRNOP00000060531; ENSRNOG00000021493. [P0C6Y7-1]
GeneIDi365155.
KEGGirno:365155.
UCSCiRGD:1305247. rat. [P0C6Y7-1]

Organism-specific databases

CTDi56979.
RGDi1305247. Prdm9.

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
KOG2461. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000234617.
HOVERGENiHBG108291.
InParanoidiP0C6Y7.
OMAiRSCNDKT.
OrthoDBiEOG7KSX7Q.
PhylomeDBiP0C6Y7.
TreeFamiTF338096.

Miscellaneous databases

NextBioi686741.
PROiP0C6Y7.

Family and domain databases

Gene3Di3.30.160.60. 10 hits.
InterProiIPR001909. KRAB.
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.
PF00856. SET. 1 hit.
PF09514. SSXRD. 1 hit.
PF00096. zf-C2H2. 7 hits.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 11 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 10 hits.
PS50157. ZINC_FINGER_C2H2_2. 10 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiPRDM9_RAT
AccessioniPrimary (citable) accession number: P0C6Y7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: February 10, 2009
Last modified: May 11, 2016
This is version 64 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.