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Q9NQV7 (PRDM9_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:PRDM9
Synonyms:PFM6
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length894 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Catalytic activity

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

Subcellular location

Nucleus By similarity. Chromosome By similarity.

Sequence similarities

Belongs to the class V-like SAM-binding methyltransferase superfamily.

Contains 14 C2H2-type zinc fingers.

Contains 1 KRAB-related domain.

Contains 1 SET domain.

Sequence caution

The sequence AAF87242.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 894894Histone-lysine N-methyltransferase PRDM9
PRO_0000047766

Regions

Domain23 – 8664KRAB-related
Domain244 – 358115SET
Zinc finger388 – 41124C2H2-type 1
Zinc finger524 – 54623C2H2-type 2; degenerate
Zinc finger552 – 57423C2H2-type 3
Zinc finger580 – 60223C2H2-type 4
Zinc finger608 – 63023C2H2-type 5
Zinc finger636 – 65823C2H2-type 6
Zinc finger664 – 68623C2H2-type 7
Zinc finger692 – 71423C2H2-type 8
Zinc finger720 – 74223C2H2-type 9
Zinc finger748 – 77023C2H2-type 10
Zinc finger776 – 79823C2H2-type 11
Zinc finger804 – 82623C2H2-type 12
Zinc finger832 – 85423C2H2-type 13
Zinc finger860 – 88223C2H2-type 14

Natural variations

Natural variant3351Y → H Common polymorphism; may be a genetic risk for patients with azoospermia caused by meiotic arrest. Ref.5
VAR_054417

Experimental info

Sequence conflict2951I → VRRACHF in AAF87242. Ref.4
Sequence conflict377 – 3815Missing in AAF87242. Ref.4
Sequence conflict6811T → S in BAG63234. Ref.2

Secondary structure

............................................ 894
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9NQV7 [UniParc].

Last modified November 4, 2008. Version 2.
Checksum: DE53094C32EFF83B

FASTA894103,376
        10         20         30         40         50         60 
MSPEKSQEES PEEDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR YRNVKRNYNA 

        70         80         90        100        110        120 
LITIGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ VKPPWMALRV EQRKHQKGMP 

       130        140        150        160        170        180 
KASFSNESSL KELSRTANLL NASGSEQAQK PVSPSGEAST SGQHSRLKLE LRKKETERKM 

       190        200        210        220        230        240 
YSLRERKGHA YKEVSEPQDD DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL 

       250        260        270        280        290        300 
SLPPGLRIGP SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANNG YSWLITKGRN 

       310        320        330        340        350        360 
CYEYVDGKDK SWANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG CELLVWYGDE 

       370        380        390        400        410        420 
YGQELGIKWG SKWKKELMAG REPKPEIHPC PSCCLAFSSQ KFLSQHVERN HSSQNFPGPS 

       430        440        450        460        470        480 
ARKLLQPENP CPGDQNQEQQ YPDPHSRNDK TKGQEIKERS KLLNKRTWQR EISRAFSSPP 

       490        500        510        520        530        540 
KGQMGSCRVG KRIMEEESRT GQKVNPGNTG KLFVGVGISR IAKVKYGECG QGFSVKSDVI 

       550        560        570        580        590        600 
THQRTHTGEK LYVCRECGRG FSWKSHLLIH QRIHTGEKPY VCRECGRGFS WQSVLLTHQR 

       610        620        630        640        650        660 
THTGEKPYVC RECGRGFSRQ SVLLTHQRRH TGEKPYVCRE CGRGFSRQSV LLTHQRRHTG 

       670        680        690        700        710        720 
EKPYVCRECG RGFSWQSVLL THQRTHTGEK PYVCRECGRG FSWQSVLLTH QRTHTGEKPY 

       730        740        750        760        770        780 
VCRECGRGFS NKSHLLRHQR THTGEKPYVC RECGRGFRDK SHLLRHQRTH TGEKPYVCRE 

       790        800        810        820        830        840 
CGRGFRDKSN LLSHQRTHTG EKPYVCRECG RGFSNKSHLL RHQRTHTGEK PYVCRECGRG 

       850        860        870        880        890 
FRNKSHLLRH QRTHTGEKPY VCRECGRGFS DRSSLCYHQR THTGEKPYVC REDE 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and characterization of PR domain-containing 9 (PRDM9)."
Ying J., Wong A.H.Y., Li H., Wang Y., Tao Q.
Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Testis.
[3]"The DNA sequence and comparative analysis of human chromosome 5."
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S. expand/collapse author list , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The yin-yang of PR-domain family genes in tumorigenesis."
Jiang G.L., Huang S.
Histol. Histopathol. 15:109-117(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 205-894.
[5]"Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest."
Miyamoto T., Koh E., Sakugawa N., Sato H., Hayashi H., Namiki M., Sengoku K.
J. Assist. Reprod. Genet. 25:553-557(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT HIS-335.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
DQ388610 mRNA. Translation: ABD47939.1.
AK301776 mRNA. Translation: BAG63234.1.
AC025451 Genomic DNA. No translation available.
AF275816 mRNA. Translation: AAF87242.1. Different initiation.
RefSeqNP_064612.2. NM_020227.2.
UniGeneHs.283096.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4IJDX-ray2.15A/B195-415[»]
ProteinModelPortalQ9NQV7.
SMRQ9NQV7. Positions 21-73, 195-892.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000296682.

PTM databases

PhosphoSiteQ9NQV7.

Polymorphism databases

DMDM212276459.

Proteomic databases

PaxDbQ9NQV7.
PRIDEQ9NQV7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000296682; ENSP00000296682; ENSG00000164256.
GeneID56979.
KEGGhsa:56979.
UCSCuc003jgo.3. human.

Organism-specific databases

CTD56979.
GeneCardsGC05P023558.
HGNCHGNC:13994. PRDM9.
HPAHPA059555.
MIM609760. gene.
neXtProtNX_Q9NQV7.
PharmGKBPA33721.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5048.
HOGENOMHOG000234617.
HOVERGENHBG108291.
InParanoidQ9NQV7.
OMARECGWGF.
OrthoDBEOG7KSX7Q.
PhylomeDBQ9NQV7.
TreeFamTF338096.

Enzyme and pathway databases

ReactomeREACT_111183. Meiosis.

Gene expression databases

ArrayExpressQ9NQV7.
BgeeQ9NQV7.
CleanExHS_PRDM9.
GenevestigatorQ9NQV7.

Family and domain databases

Gene3D3.30.160.60. 13 hits.
InterProIPR001909. Krueppel-associated_box.
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]
PfamPF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
[Graphical view]
SMARTSM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 14 hits.
[Graphical view]
SUPFAMSSF109640. SSF109640. 1 hit.
PROSITEPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 13 hits.
PS50157. ZINC_FINGER_C2H2_2. 14 hits.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiPRDM9.
GenomeRNAi56979.
NextBio62639.
PROQ9NQV7.
SOURCESearch...

Entry information

Entry namePRDM9_HUMAN
AccessionPrimary (citable) accession number: Q9NQV7
Secondary accession number(s): B4DX22, Q27Q50
Entry history
Integrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: November 4, 2008
Last modified: April 16, 2014
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 5

Human chromosome 5: entries, gene names and cross-references to MIM