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Protein

Histone-lysine N-methyltransferase PRDM9

Gene

PRDM9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 + N6-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

  • histone-lysine N-methyltransferase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • recombination hotspot binding Source: UniProtKB
  • RNA polymerase II transcription factor activity, sequence-specific DNA binding Source: NTNU_SB
  • sequence-specific DNA binding Source: UniProtKB
  • transcription regulatory region DNA binding Source: UniProtKB

GO - Biological processi

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

Keywordsi

Molecular functionActivator, Chromatin regulator, Methyltransferase, Transferase
Biological processMeiosis, Transcription, Transcription regulation
LigandMetal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000164256.10
HGNCiHGNC:13994 PRDM9
MIMi609760 gene
neXtProtiNX_Q9NQV7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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

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
GeneTreeiENSGT00830000128341
HOGENOMiHOG000234617
HOVERGENiHBG108291
InParanoidiQ9NQV7
KOiK20796
OMAiRSCNDKT
OrthoDBiEOG091G02KC
PhylomeDBiQ9NQV7
TreeFamiTF338096

Family and domain databases

CDDicd07765 KRAB_A-box, 1 hit
InterProiView protein in InterPro
IPR001909 KRAB
IPR036051 KRAB_dom_sf
IPR003655 Krueppel-associated_box-rel
IPR001214 SET_dom
IPR019041 SSXRD_motif
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF01352 KRAB, 1 hit
PF00856 SET, 1 hit
PF09514 SSXRD, 1 hit
SMARTiView protein in SMART
SM00349 KRAB, 1 hit
SM00355 ZnF_C2H2, 14 hits
SUPFAMiSSF109640 SSF109640, 1 hit
SSF57667 SSF57667, 7 hits
PROSITEiView protein in PROSITE
PS50806 KRAB_RELATED, 1 hit
PS50280 SET, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 13 hits
PS50157 ZINC_FINGER_C2H2_2, 14 hits

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

Similar proteinsi

Entry informationi

Entry nameiPRDM9_HUMAN
AccessioniPrimary (citable) accession number: Q9NQV7
Secondary accession number(s): B4DX22, Q27Q50
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: November 4, 2008
Last modified: May 23, 2018
This is version 149 of the entry and version 2 of the sequence. See 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
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Main funding by: National Institutes of Health