{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"Q9NQV7","secondaryAccessions":["B4DX22","Q27Q50"],"uniProtkbId":"PRDM9_HUMAN","entryAudit":{"firstPublicDate":"2001-11-16","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"2008-11-04","entryVersion":196,"sequenceVersion":2},"annotationScore":5.0,"organism":{"scientificName":"Homo sapiens","commonName":"Human","taxonId":9606,"lineage":["Eukaryota","Metazoa","Chordata","Craniata","Vertebrata","Euteleostomi","Mammalia","Eutheria","Euarchontoglires","Primates","Haplorrhini","Catarrhini","Hominidae","Homo"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Histone-lysine N-methyltransferase PRDM9"}},"alternativeNames":[{"fullName":{"value":"PR domain zinc finger protein 9"}},{"fullName":{"value":"PR domain-containing protein 9"}},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"Protein-lysine N-methyltransferase PRDM9"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"2.1.1.-"}]},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"[histone H3]-lysine36 N-trimethyltransferase PRDM9"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24634223"}],"value":"2.1.1.359"}]},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"[histone H3]-lysine4 N-trimethyltransferase PRDM9"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24095733"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24634223"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26833727"}],"value":"2.1.1.354"}]},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"[histone H3]-lysine9 N-trimethyltransferase PRDM9"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"2.1.1.355"}]},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"[histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"2.1.1.362"}]},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"[histone H4]-lysine20 N-methyltransferase PRDM9"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"2.1.1.361"}]}]},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000312","source":"HGNC","id":"HGNC:13994"}],"value":"PRDM9"},"synonyms":[{"value":"PFM6"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"18941885"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24095733"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24634223"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26833727"}],"value":"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:18941885, PubMed:24095733, PubMed:24634223, PubMed:26833727, PubMed:27129774). Can also 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)"}],"commentType":"FUNCTION"},{"commentType":"CATALYTIC ACTIVITY","reaction":{"name":"L-lysyl-[protein] + S-adenosyl-L-methionine = N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:51736"},{"database":"Rhea","id":"RHEA-COMP:9752"},{"database":"Rhea","id":"RHEA-COMP:13053"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:29969"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:61929"}],"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}]},"physiologicalReactions":[{"directionType":"left-to-right","reactionCrossReference":{"database":"Rhea","id":"RHEA:51737"},"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}]}]},{"commentType":"CATALYTIC 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8.5."}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24095733"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26833727"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32001511"},{"evidenceCode":"ECO:0000269","source":"Reference","id":"Ref.10"}],"value":"Homodimer (PubMed:24095733, PubMed:26833727, Ref.10). 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). Interacts with HELLS; the interaction recruits HELLS to meiotic recombination hot spots (PubMed:32001511)"}],"commentType":"SUBUNIT"},{"commentType":"SUBCELLULAR LOCATION","note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"Localizes in nuclei of pre-leptotene, leptotene, and early to mid-zygotene spermatocytes"}]},"subcellularLocations":[{"location":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"Nucleus","id":"SL-0191"}},{"location":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"Chromosome","id":"SL-0468"}}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"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"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96EQ9"}],"value":"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"}],"commentType":"PTM"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26833727"}],"value":"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"}],"commentType":"POLYMORPHISM"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU00190"}],"value":"Belongs to the class V-like SAM-binding methyltransferase superfamily"}],"commentType":"SIMILARITY"},{"commentType":"SEQUENCE CAUTION","sequenceCautionType":"Erroneous initiation","sequence":"AAF87242.1","note":"Truncated N-terminus.","evidences":[{"evidenceCode":"ECO:0000305"}]}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":894,"modifier":"EXACT"}},"description":"Histone-lysine N-methyltransferase 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