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Entry version 169 (07 Oct 2020)
Sequence version 2 (04 Nov 2008)
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Protein

Histone-lysine N-methyltransferase PRDM9

Gene

PRDM9

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

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Histone methyltransferase that sequentially mono-, di-, and tri-methylates both 'Lys-4' (H3K4) and 'Lys-36' (H3K36) of histone H3 to produce respectively trimethylated 'Lys-4' (H3K4me3) and trimethylated 'Lys-36' (H3K36me3) histone H3 and plays a key role in meiotic prophase by determining hotspot localization thereby promoting meiotic recombination (PubMed:24634223, PubMed:24095733, PubMed:26833727). Also can methylate all four core histones with H3 being the best substrate and the most highly modified (PubMed:24095733, PubMed:24634223, PubMed:26833727). Is also able, on one hand, to mono and di-methylate H4K20 and on other hand to trimethylate H3K9 with the di-methylated H3K9 as the best substrate (By similarity). During meiotic prophase, binds specific DNA sequences through its zinc finger domains thereby determining hotspot localization where it promotes local H3K4me3 and H3K36me3 enrichment on the same nucleosomes through its histone methyltransferase activity (PubMed:26833727). Thereby promotes double-stranded breaks (DSB) formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression (By similarity). During meiotic progression hotspot-bound PRDM9 interacts with several complexes; in early leptonema binds CDYL and EHMT2 followed by EWSR1 and CXXC1 by the end of leptonema. EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity). In this way, controls the DSB repair pathway, pairing of homologous chromosomes and sex body formation (By similarity). Moreover plays a central role in the transcriptional activation of genes during early meiotic prophase thanks to H3K4me3 and H3K36me3 enrichment that represents a specific tag for epigenetic transcriptional activation (By similarity). In addition performs automethylation (By similarity). Acetylation and phosphorylation of histone H3 attenuate or prevent histone H3 methylation (By similarity).By similarity3 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Inhibited by suramin with an IC50 of 4.1 µM.1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

All kinetic experiments are done with 10 mm Tris-HCl, 0.01% Triton X-100, and 10 mm DTT and at pH 8.5.1 Publication
  1. KM=1 µM for H3K4me01 Publication
  2. KM=1 µM for H3K4me11 Publication
  3. KM=3 µM for H3K4me21 Publication
  4. KM=1.5 µM for H3K36me01 Publication
  5. KM=2.4 µM for H3K36me11 Publication
  6. KM=2.5 µM for H3K36me21 Publication
  7. KM=0.7 µM for native H3-H4 tetramer1 Publication
  8. KM=120 µM for S-adenosyl-L-methionine (with H3K4me0 as substrate)1 Publication
  9. KM=170 µM for S-adenosyl-L-methionine (with H3K4me1 as substrate)1 Publication
  10. KM=140 µM for S-adenosyl-L-methionine (with H3K4me2 as substrate)1 Publication
  11. KM=87 µM for S-adenosyl-L-methionine (with H3K36me0 as substrate)1 Publication
  12. KM=130 µM for S-adenosyl-L-methionine (with H3K36me1 as substrate)1 Publication
  13. KM=62 µM for S-adenosyl-L-methionine (with H3K36me2 as substrate)1 Publication
  14. KM=240 µM for S-adenosyl-L-methionine (with native H3-H4 tetramer as substrate)1 Publication

    pH dependencei

    Optimum pH is 8.5.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi205Zinc 1Combined sources2 Publications1
    Metal bindingi208Zinc 1Combined sources2 Publications1
    Metal bindingi216Zinc 1Combined sources2 Publications1
    Metal bindingi219Zinc 1; via pros nitrogenCombined sources2 Publications1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei291S-adenosyl-L-methionine1 Publication1
    Binding sitei357SubstrateBy similarity1
    Metal bindingi390Zinc 2Combined sources1 Publication1
    Metal bindingi393Zinc 2Combined sources1 Publication1
    Metal bindingi406Zinc 2; via tele nitrogenCombined sources1 Publication1
    Metal bindingi411Zinc 2; via tele nitrogenCombined sources1 Publication1
    Metal bindingi722Zinc 3Combined sources1 Publication1
    Metal bindingi725Zinc 3Combined sources1 Publication1
    Metal bindingi738Zinc 3; via tele nitrogenCombined sources1 Publication1
    Metal bindingi742Zinc 3; via tele nitrogenCombined sources1 Publication1
    Metal bindingi750Zinc 4Combined sources1 Publication1
    Metal bindingi753Zinc 4Combined sources1 Publication1
    Metal bindingi766Zinc 4; via tele nitrogenCombined sources1 Publication1
    Metal bindingi770Zinc 4; via tele nitrogenCombined sources1 Publication1
    Metal bindingi778Zinc 5Combined sources1 Publication1
    Metal bindingi781Zinc 5Combined sources1 Publication1
    Metal bindingi794Zinc 5; via tele nitrogenCombined sources1 Publication1
    Metal bindingi798Zinc 5; via tele nitrogenCombined sources1 Publication1
    Metal bindingi806Zinc 6Combined sources1 Publication1
    Metal bindingi809Zinc 6Combined sources1 Publication1
    Metal bindingi822Zinc 6; via tele nitrogenCombined sources1 Publication1
    Metal bindingi826Zinc 6; via tele nitrogenCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>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

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:HS09047-MONOMER

    Pathway Commons web resource for biological pathway data

    More...
    PathwayCommonsi
    Q9NQV7

    Reactome - a knowledgebase of biological pathways and processes

    More...
    Reactomei
    R-HSA-3214841, PKMTs methylate histone lysines
    R-HSA-912446, Meiotic recombination

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Histone-lysine N-methyltransferase PRDM9Curated
    Alternative name(s):
    PR domain zinc finger protein 9
    PR domain-containing protein 9
    Protein-lysine N-methyltransferase PRDM9By similarity (EC:2.1.1.-By similarity)
    [histone H3]-lysine36 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3591 Publication)
    [histone H3]-lysine4 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3543 Publications)
    [histone H3]-lysine9 N-trimethyltransferase PRDM9By similarity (EC:2.1.1.355By similarity)
    [histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9By similarity (EC:2.1.1.362By similarity)
    [histone H4]-lysine20 N-methyltransferase PRDM9By similarity (EC:2.1.1.361By similarity)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:PRDM9Imported
    Synonyms:PFM6
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHomo sapiens (Human)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri9606 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 5

    Organism-specific databases

    Eukaryotic Pathogen Database Resources

    More...
    EuPathDBi
    HostDB:ENSG00000164256.10

    Human Gene Nomenclature Database

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    HGNCi
    HGNC:13994, PRDM9

    Online Mendelian Inheritance in Man (OMIM)

    More...
    MIMi
    609760, gene

    neXtProt; the human protein knowledge platform

    More...
    neXtProti
    NX_Q9NQV7

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>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 & Seán O’Donoghue; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Chromosome, Nucleus

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi199D → Y: Increases histone-lysine N-methyltransferase activity; when associated with D-374. 1 Publication1
    Mutagenesisi374K → D: Increases histone-lysine N-methyltransferase activity; when associated with Y-199. 1 Publication1

    Organism-specific databases

    DisGeNET

    More...
    DisGeNETi
    56979

    Open Targets

    More...
    OpenTargetsi
    ENSG00000164256

    The Pharmacogenetics and Pharmacogenomics Knowledge Base

    More...
    PharmGKBi
    PA33721

    Miscellaneous databases

    Pharos NIH Druggable Genome Knowledgebase

    More...
    Pharosi
    Q9NQV7, Tbio

    Chemistry databases

    ChEMBL database of bioactive drug-like small molecules

    More...
    ChEMBLi
    CHEMBL3588737

    Polymorphism and mutation databases

    BioMuta curated single-nucleotide variation and disease association database

    More...
    BioMutai
    PRDM9

    Domain mapping of disease mutations (DMDM)

    More...
    DMDMi
    212276459

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000477661 – 894Histone-lysine N-methyltransferase PRDM9Add BLAST894

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei368N6,N6,N6-trimethyllysine; alternateBy similarity1
    Modified residuei368N6-methyllysine; alternateBy similarity1
    Modified residuei372N6-methyllysineBy similarity1
    Modified residuei374N6-methyllysineBy similarity1

    <p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

    Mono-methylated; automethylated. Tri-methylated; automethylated. Mono-methylation is predominant; automethylation is lower and slower than H3 peptide methylation and is in a highest S-adenosyl-L-methionine concentration-dependent. There are two major sites for automethylation at Lys-368 and Lys-374. Lysines can be simultaneously methylated, such as Lys-368(me3)/Lys-372(me1), Lys-368(me1)/Lys-374(me1) and Lys-368(me1)/Lys-372(me1)/Lys-374(me1). Automethylation is an intramolecular (cis) process.By similarity

    Keywords - PTMi

    Methylation

    Proteomic databases

    MassIVE - Mass Spectrometry Interactive Virtual Environment

    More...
    MassIVEi
    Q9NQV7

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    Q9NQV7

    PeptideAtlas

    More...
    PeptideAtlasi
    Q9NQV7

    PRoteomics IDEntifications database

    More...
    PRIDEi
    Q9NQV7

    ProteomicsDB: a multi-organism proteome resource

    More...
    ProteomicsDBi
    82198

    PTM databases

    iPTMnet integrated resource for PTMs in systems biology context

    More...
    iPTMneti
    Q9NQV7

    Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

    More...
    PhosphoSitePlusi
    Q9NQV7

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    Gene expression databases

    Bgee dataBase for Gene Expression Evolution

    More...
    Bgeei
    ENSG00000164256, Expressed in testis and 61 other tissues

    ExpressionAtlas, Differential and Baseline Expression

    More...
    ExpressionAtlasi
    Q9NQV7, baseline and differential

    Genevisible search portal to normalized and curated expression data from Genevestigator

    More...
    Genevisiblei
    Q9NQV7, HS

    Organism-specific databases

    Human Protein Atlas

    More...
    HPAi
    ENSG00000164256, Tissue enhanced (blood, epididymis, testis)

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer (PubMed:26833727, PubMed:24095733, Ref. 9).

    Interacts with EHMT2 and CDYL; interaction only takes place when PRDM9 is bound to hotspot DNA.

    Interacts with CXXC1; this interaction does not link PRDM9-activated recombination hotspot sites with DSB machinery and is not required for the hotspot recognition pathway.

    Forms a complex with EWSR1, REC8, SYCP3 and SYCP1; complex formation is dependent of phosphorylated form of REC8 and requires PRDM9 bound to hotspot DNA; EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity).

    By similarity3 Publications

    GO - Molecular functioni

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGRID)

    More...
    BioGRIDi
    121297, 1 interactor

    Protein interaction database and analysis system

    More...
    IntActi
    Q9NQV7, 1 interactor

    STRING: functional protein association networks

    More...
    STRINGi
    9606.ENSP00000296682

    Miscellaneous databases

    RNAct, Protein-RNA interaction predictions for model organisms.

    More...
    RNActi
    Q9NQV7, protein

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1894
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q9NQV7

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini23 – 86KRAB-relatedPROSITE-ProRule annotationAdd BLAST64
    Domaini244 – 358SETPROSITE-ProRule annotationAdd BLAST115

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni256 – 258S-adenosyl-L-methionine binding1 Publication3
    Regioni288 – 294Substrate bindingBy similarity7
    Regioni320 – 321S-adenosyl-L-methionine binding1 Publication2
    Regioni730 – 820DNA-binding1 PublicationAdd BLAST91

    <p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

    The C2H2-type zinc fingers determine the hotspot localization through its binding to specific DNA sequences. Variations in their sequence affect affinity towards DNA-binding motif.By similarity

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>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

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    KOG1721, Eukaryota
    KOG2461, Eukaryota

    Ensembl GeneTree

    More...
    GeneTreei
    ENSGT00940000163405

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_002678_32_0_1

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    Q9NQV7

    KEGG Orthology (KO)

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    KOi
    K20796

    Identification of Orthologs from Complete Genome Data

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    OMAi
    RSCNDKT

    Database of Orthologous Groups

    More...
    OrthoDBi
    1318335at2759

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    Q9NQV7

    TreeFam database of animal gene trees

    More...
    TreeFami
    TF338096

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd07765, KRAB_A-box, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View 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

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01352, KRAB, 1 hit
    PF00856, SET, 1 hit
    PF09514, SSXRD, 1 hit
    PF00096, zf-C2H2, 9 hits

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00349, KRAB, 1 hit
    SM00355, ZnF_C2H2, 14 hits

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF109640, SSF109640, 1 hit
    SSF57667, SSF57667, 7 hits

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View 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

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

    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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDE53094C32EFF83B
    GO

    <p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

    There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
    EntryEntry nameProtein names
    Gene namesLengthAnnotation
    D6RD68D6RD68_HUMAN
    Histone-lysine N-methyltransferase ...
    PRDM9
    100Annotation score:

    Annotation score:1 out of 5

    <p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
    A0A0U1RQY2A0A0U1RQY2_HUMAN
    Histone-lysine N-methyltransferase ...
    PRDM9
    411Annotation score:

    Annotation score:1 out of 5

    <p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

    <p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

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

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti295I → VRRACHF in AAF87242 (PubMed:10668202).Curated1
    Sequence conflicti377 – 381Missing in AAF87242 (PubMed:10668202).Curated5

    <p>This subsection of the 'Sequence' section provides information on polymorphic variants. If the variant is associated with a disease state, the description of the latter can be found in the <a href="http://www.uniprot.org/manual/involvement%5Fin%5Fdisease">'Involvement in disease'</a> subsection.<p><a href='/help/polymorphism' target='_top'>More...</a></p>Polymorphismi

    Several alleles exist depending on both the number of zinc finger C2H2 type domains and their identity (PubMed:26833727). Each allele binds to a specific hotspot set (PubMed:26833727). Variations in the zinc finger C2H2 type domains are associated with significant differences in affinity towards DNA-binding motif (PubMed:26833727). The sequence shown is that of allele B.1 Publication

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Sequence' section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural variantiVAR_054417335Y → H Common polymorphism; may be a genetic risk for patients with azoospermia caused by meiotic arrest. 1 Publication1
    Natural variantiVAR_082281681T → S in allele A. 1 PublicationCorresponds to variant dbSNP:rs6875787EnsemblClinVar.1
    Natural variantiVAR_082282788K → E in allele L9/24; significantly reduces affinity for the DNA-binding motif 5'-GCCTCCCTAGCCACG-3'. 1 PublicationCorresponds to variant dbSNP:rs146505774Ensembl.1
    Natural variantiVAR_082283790N → H in allele L20; reduces affinity for the DNA-binding motif 5?-GCCTCCCTAGCCACG-3'. 1 PublicationCorresponds to variant dbSNP:rs77287813EnsemblClinVar.1
    Natural variantiVAR_082284814S → R in allele L13; Increases affinity for the DNA-binding motif 5'-GCCTCCCTAGCCACG-3'. 1 PublicationCorresponds to variants dbSNP:rs1445421439 and dbSNP:rs61051796EnsemblEnsembl.1

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    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.

    The Consensus CDS (CCDS) project

    More...
    CCDSi
    CCDS43307.1

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_001297143.1, NM_001310214.1
    NP_064612.2, NM_020227.3

    Genome annotation databases

    Ensembl eukaryotic genome annotation project

    More...
    Ensembli
    ENST00000296682; ENSP00000296682; ENSG00000164256

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    56979

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    hsa:56979

    UCSC genome browser

    More...
    UCSCi
    uc003jgo.3, human

    Keywords - Coding sequence diversityi

    Polymorphism

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    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[»]
    6NM4X-ray2.58A/B195-385[»]
    SMRiQ9NQV7
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    BioGRIDi121297, 1 interactor
    IntActiQ9NQV7, 1 interactor
    STRINGi9606.ENSP00000296682

    Chemistry databases

    ChEMBLiCHEMBL3588737

    PTM databases

    iPTMnetiQ9NQV7
    PhosphoSitePlusiQ9NQV7

    Polymorphism and mutation databases

    BioMutaiPRDM9
    DMDMi212276459

    Proteomic databases

    MassIVEiQ9NQV7
    PaxDbiQ9NQV7
    PeptideAtlasiQ9NQV7
    PRIDEiQ9NQV7
    ProteomicsDBi82198

    Protocols and materials databases

    Antibodypedia a portal for validated antibodies

    More...
    Antibodypediai
    22638, 79 antibodies

    Genome annotation databases

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

    Organism-specific databases

    Comparative Toxicogenomics Database

    More...
    CTDi
    56979
    DisGeNETi56979
    EuPathDBiHostDB:ENSG00000164256.10

    GeneCards: human genes, protein and diseases

    More...
    GeneCardsi
    PRDM9
    HGNCiHGNC:13994, PRDM9
    HPAiENSG00000164256, Tissue enhanced (blood, epididymis, testis)
    MIMi609760, gene
    neXtProtiNX_Q9NQV7
    OpenTargetsiENSG00000164256
    PharmGKBiPA33721

    GenAtlas: human gene database

    More...
    GenAtlasi
    Search...

    Phylogenomic databases

    eggNOGiKOG1721, Eukaryota
    KOG2461, Eukaryota
    GeneTreeiENSGT00940000163405
    HOGENOMiCLU_002678_32_0_1
    InParanoidiQ9NQV7
    KOiK20796
    OMAiRSCNDKT
    OrthoDBi1318335at2759
    PhylomeDBiQ9NQV7
    TreeFamiTF338096

    Enzyme and pathway databases

    BioCyciMetaCyc:HS09047-MONOMER
    PathwayCommonsiQ9NQV7
    ReactomeiR-HSA-3214841, PKMTs methylate histone lysines
    R-HSA-912446, Meiotic recombination

    Miscellaneous databases

    BioGRID ORCS database of CRISPR phenotype screens

    More...
    BioGRID-ORCSi
    56979, 10 hits in 871 CRISPR screens

    The Gene Wiki collection of pages on human genes and proteins

    More...
    GeneWikii
    PRDM9

    Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens

    More...
    GenomeRNAii
    56979
    PharosiQ9NQV7, Tbio

    Protein Ontology

    More...
    PROi
    PR:Q9NQV7
    RNActiQ9NQV7, protein

    The Stanford Online Universal Resource for Clones and ESTs

    More...
    SOURCEi
    Search...

    Gene expression databases

    BgeeiENSG00000164256, Expressed in testis and 61 other tissues
    ExpressionAtlasiQ9NQV7, baseline and differential
    GenevisibleiQ9NQV7, HS

    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
    PF00096, zf-C2H2, 9 hits
    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

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPRDM9_HUMAN
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9NQV7
    Secondary accession number(s): B4DX22, Q27Q50
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 16, 2001
    Last sequence update: November 4, 2008
    Last modified: October 7, 2020
    This is version 169 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>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.

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Reference proteome

    Documents

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