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Protein

Histone-lysine N-methyltransferase PRDM9

Gene

PRDM9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 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 (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)DescriptionActionsGraphical viewLength
Zinc fingeri388 – 411C2H2-type 1PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri524 – 546C2H2-type 2; degeneratePROSITE-ProRule annotationAdd BLAST23
Zinc fingeri552 – 574C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri580 – 602C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri608 – 630C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri636 – 658C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri664 – 686C2H2-type 7PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri692 – 714C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri720 – 742C2H2-type 9PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri748 – 770C2H2-type 10PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri776 – 798C2H2-type 11PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri804 – 826C2H2-type 12PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri832 – 854C2H2-type 13PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri860 – 882C2H2-type 14PROSITE-ProRule annotationAdd BLAST23

GO - Molecular functioni

GO - Biological processi

  • meiotic gene conversion Source: MGI
  • positive regulation of reciprocal meiotic recombination Source: MGI
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • 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

BioCyciZFISH:HS09047-MONOMER.
ReactomeiR-HSA-3214841. PKMTs methylate histone lysines.
R-HSA-912446. Meiotic recombination.

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
Synonyms:PFM6
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:13994. PRDM9.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi56979.
OpenTargetsiENSG00000164256.
PharmGKBiPA33721.

Chemistry databases

ChEMBLiCHEMBL3588737.

Polymorphism and mutation databases

BioMutaiPRDM9.
DMDMi212276459.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477661 – 894Histone-lysine N-methyltransferase PRDM9Add BLAST894

Proteomic databases

PaxDbiQ9NQV7.
PeptideAtlasiQ9NQV7.
PRIDEiQ9NQV7.

PTM databases

iPTMnetiQ9NQV7.
PhosphoSitePlusiQ9NQV7.

Expressioni

Gene expression databases

BgeeiENSG00000164256.
CleanExiHS_PRDM9.
ExpressionAtlasiQ9NQV7. baseline and differential.
GenevisibleiQ9NQV7. HS.

Organism-specific databases

HPAiHPA059555.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000296682.

Structurei

Secondary structure

1894
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi199 – 201Combined sources3
Beta strandi203 – 205Combined sources3
Turni206 – 209Combined sources4
Beta strandi210 – 216Combined sources7
Turni217 – 219Combined sources3
Helixi237 – 240Combined sources4
Beta strandi246 – 250Combined sources5
Beta strandi258 – 262Combined sources5
Beta strandi278 – 281Combined sources4
Helixi284 – 286Combined sources3
Beta strandi289 – 298Combined sources10
Beta strandi301 – 306Combined sources6
Turni310 – 312Combined sources3
Helixi315 – 318Combined sources4
Turni325 – 327Combined sources3
Beta strandi330 – 335Combined sources6
Beta strandi338 – 345Combined sources8
Beta strandi354 – 356Combined sources3
Helixi362 – 367Combined sources6
Turni368 – 370Combined sources3
Helixi373 – 377Combined sources5
Beta strandi391 – 394Combined sources4
Beta strandi396 – 399Combined sources4
Helixi400 – 410Combined sources11
Turni723 – 725Combined sources3
Beta strandi728 – 731Combined sources4
Helixi732 – 743Combined sources12
Turni751 – 753Combined sources3
Beta strandi756 – 759Combined sources4
Helixi760 – 765Combined sources6
Helixi768 – 771Combined sources4
Turni779 – 781Combined sources3
Beta strandi784 – 787Combined sources4
Helixi788 – 799Combined sources12
Turni807 – 809Combined sources3
Beta strandi812 – 815Combined sources4
Helixi816 – 823Combined sources8
Turni824 – 826Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IJDX-ray2.15A/B195-415[»]
5EGBX-ray1.98A717-858[»]
5EH2X-ray2.05E/F717-858[»]
5EI9X-ray1.92E/F717-858[»]
ProteinModelPortaliQ9NQV7.
SMRiQ9NQV7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini23 – 86KRAB-relatedPROSITE-ProRule annotationAdd BLAST64
Domaini244 – 358SETPROSITE-ProRule annotationAdd BLAST115

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 14 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)DescriptionActionsGraphical viewLength
Zinc fingeri388 – 411C2H2-type 1PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri524 – 546C2H2-type 2; degeneratePROSITE-ProRule annotationAdd BLAST23
Zinc fingeri552 – 574C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri580 – 602C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri608 – 630C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri636 – 658C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri664 – 686C2H2-type 7PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri692 – 714C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri720 – 742C2H2-type 9PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri748 – 770C2H2-type 10PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri776 – 798C2H2-type 11PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri804 – 826C2H2-type 12PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri832 – 854C2H2-type 13PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri860 – 882C2H2-type 14PROSITE-ProRule annotationAdd BLAST23

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00530000063157.
HOGENOMiHOG000234617.
HOVERGENiHBG108291.
InParanoidiQ9NQV7.
KOiK20796.
OMAiRSCNDKT.
OrthoDBiEOG091G02KC.
PhylomeDBiQ9NQV7.
TreeFamiTF338096.

Family and domain databases

CDDicd07765. KRAB_A-box. 1 hit.
Gene3Di3.30.160.60. 13 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. 5 hits.
PF13912. zf-C2H2_6. 2 hits.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00355. ZnF_C2H2. 14 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 13 hits.
PS50157. ZINC_FINGER_C2H2_2. 14 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9NQV7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPEKSQEES PEEDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR
60 70 80 90 100
YRNVKRNYNA LITIGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ
110 120 130 140 150
VKPPWMALRV EQRKHQKGMP KASFSNESSL KELSRTANLL NASGSEQAQK
160 170 180 190 200
PVSPSGEAST SGQHSRLKLE LRKKETERKM YSLRERKGHA YKEVSEPQDD
210 220 230 240 250
DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL SLPPGLRIGP
260 270 280 290 300
SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANNG YSWLITKGRN
310 320 330 340 350
CYEYVDGKDK SWANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG
360 370 380 390 400
CELLVWYGDE YGQELGIKWG SKWKKELMAG REPKPEIHPC PSCCLAFSSQ
410 420 430 440 450
KFLSQHVERN HSSQNFPGPS ARKLLQPENP CPGDQNQEQQ YPDPHSRNDK
460 470 480 490 500
TKGQEIKERS KLLNKRTWQR EISRAFSSPP KGQMGSCRVG KRIMEEESRT
510 520 530 540 550
GQKVNPGNTG KLFVGVGISR IAKVKYGECG QGFSVKSDVI THQRTHTGEK
560 570 580 590 600
LYVCRECGRG FSWKSHLLIH QRIHTGEKPY VCRECGRGFS WQSVLLTHQR
610 620 630 640 650
THTGEKPYVC RECGRGFSRQ SVLLTHQRRH TGEKPYVCRE CGRGFSRQSV
660 670 680 690 700
LLTHQRRHTG EKPYVCRECG RGFSWQSVLL THQRTHTGEK PYVCRECGRG
710 720 730 740 750
FSWQSVLLTH QRTHTGEKPY VCRECGRGFS NKSHLLRHQR THTGEKPYVC
760 770 780 790 800
RECGRGFRDK SHLLRHQRTH TGEKPYVCRE CGRGFRDKSN LLSHQRTHTG
810 820 830 840 850
EKPYVCRECG RGFSNKSHLL RHQRTHTGEK PYVCRECGRG FRNKSHLLRH
860 870 880 890
QRTHTGEKPY VCRECGRGFS DRSSLCYHQR THTGEKPYVC REDE
Length:894
Mass (Da):103,376
Last modified:November 4, 2008 - v2
Checksum:iDE53094C32EFF83B
GO

Sequence cautioni

The sequence AAF87242 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti295I → VRRACHF in AAF87242 (PubMed:10668202).Curated1
Sequence conflicti377 – 381Missing in AAF87242 (PubMed:10668202).Curated5
Sequence conflicti681T → S in BAG63234 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_054417335Y → H Common polymorphism; may be a genetic risk for patients with azoospermia caused by meiotic arrest. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ388610 mRNA. Translation: ABD47939.1.
AK301776 mRNA. Translation: BAG63234.1.
AC025451 Genomic DNA. No translation available.
AF275816 mRNA. Translation: AAF87242.1. Different initiation.
CCDSiCCDS43307.1.
RefSeqiNP_001297143.1. NM_001310214.1.
NP_064612.2. NM_020227.3.
UniGeneiHs.283096.

Genome annotation databases

EnsembliENST00000296682; ENSP00000296682; ENSG00000164256.
GeneIDi56979.
KEGGihsa:56979.
UCSCiuc003jgo.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ388610 mRNA. Translation: ABD47939.1.
AK301776 mRNA. Translation: BAG63234.1.
AC025451 Genomic DNA. No translation available.
AF275816 mRNA. Translation: AAF87242.1. Different initiation.
CCDSiCCDS43307.1.
RefSeqiNP_001297143.1. NM_001310214.1.
NP_064612.2. NM_020227.3.
UniGeneiHs.283096.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IJDX-ray2.15A/B195-415[»]
5EGBX-ray1.98A717-858[»]
5EH2X-ray2.05E/F717-858[»]
5EI9X-ray1.92E/F717-858[»]
ProteinModelPortaliQ9NQV7.
SMRiQ9NQV7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000296682.

Chemistry databases

ChEMBLiCHEMBL3588737.

PTM databases

iPTMnetiQ9NQV7.
PhosphoSitePlusiQ9NQV7.

Polymorphism and mutation databases

BioMutaiPRDM9.
DMDMi212276459.

Proteomic databases

PaxDbiQ9NQV7.
PeptideAtlasiQ9NQV7.
PRIDEiQ9NQV7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000296682; ENSP00000296682; ENSG00000164256.
GeneIDi56979.
KEGGihsa:56979.
UCSCiuc003jgo.3. human.

Organism-specific databases

CTDi56979.
DisGeNETi56979.
GeneCardsiPRDM9.
HGNCiHGNC:13994. PRDM9.
HPAiHPA059555.
MIMi609760. gene.
neXtProtiNX_Q9NQV7.
OpenTargetsiENSG00000164256.
PharmGKBiPA33721.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00530000063157.
HOGENOMiHOG000234617.
HOVERGENiHBG108291.
InParanoidiQ9NQV7.
KOiK20796.
OMAiRSCNDKT.
OrthoDBiEOG091G02KC.
PhylomeDBiQ9NQV7.
TreeFamiTF338096.

Enzyme and pathway databases

BioCyciZFISH:HS09047-MONOMER.
ReactomeiR-HSA-3214841. PKMTs methylate histone lysines.
R-HSA-912446. Meiotic recombination.

Miscellaneous databases

GeneWikiiPRDM9.
GenomeRNAii56979.
PROiQ9NQV7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000164256.
CleanExiHS_PRDM9.
ExpressionAtlasiQ9NQV7. baseline and differential.
GenevisibleiQ9NQV7. HS.

Family and domain databases

CDDicd07765. KRAB_A-box. 1 hit.
Gene3Di3.30.160.60. 13 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. 5 hits.
PF13912. zf-C2H2_6. 2 hits.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00355. ZnF_C2H2. 14 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 13 hits.
PS50157. ZINC_FINGER_C2H2_2. 14 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRDM9_HUMAN
AccessioniPrimary (citable) accession number: Q9NQV7
Secondary accession number(s): B4DX22, Q27Q50
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: November 4, 2008
Last modified: November 30, 2016
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.