Q9NQV7 (PRDM9_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	PRDM9
Synonyms:	PFM6

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	894 AA.
Sequence status	Complete.
Protein existence	Evidence 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	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.

Ontologies

Keywords
Biological process	Meiosis Transcription Transcription regulation
Cellular component	Chromosome Nucleus
Coding sequence diversity	Polymorphism
Domain	Repeat Zinc-finger
Ligand	Metal-binding S-adenosyl-L-methionine Zinc
Molecular function	Activator Chromatin regulator Methyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	meiotic gene conversion Inferred from direct assay PubMed 21750151. Source: MGI meiotic prophase I Inferred from electronic annotation. Source: Compara positive regulation of reciprocal meiotic recombination Inferred from mutant phenotype PubMed 21750151. Source: MGI positive regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara spermatogenesis Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	chromosome Inferred from electronic annotation. Source: UniProtKB-SubCell nucleoplasm Traceable author statement. Source: Reactome
Molecular_function	histone methyltransferase activity (H3-K4 specific) Inferred from electronic annotation. Source: Compara recombination hotspot binding Inferred from electronic annotation. Source: Compara sequence-specific DNA binding Inferred from electronic annotation. Source: Compara zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 894

894

Histone-lysine N-methyltransferase PRDM9

PRO_0000047766

Regions

Domain

23 – 86

64

KRAB-related

Domain

246 – 362

117

SET

Zinc finger

388 – 411

24

C2H2-type 1

Zinc finger

524 – 546

23

C2H2-type 2; degenerate

Zinc finger

552 – 574

23

C2H2-type 3

Zinc finger

580 – 602

23

C2H2-type 4

Zinc finger

608 – 630

23

C2H2-type 5

Zinc finger

636 – 658

23

C2H2-type 6

Zinc finger

664 – 686

23

C2H2-type 7

Zinc finger

692 – 714

23

C2H2-type 8

Zinc finger

720 – 742

23

C2H2-type 9

Zinc finger

748 – 770

23

C2H2-type 10

Zinc finger

776 – 798

23

C2H2-type 11

Zinc finger

804 – 826

23

C2H2-type 12

Zinc finger

832 – 854

23

C2H2-type 13

Zinc finger

860 – 882

23

C2H2-type 14

Natural variations

Natural variant

335

1

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

VAR_054417

Experimental info

Sequence conflict

295

1

I → VRRACHF in AAF87242. Ref.4

Sequence conflict

377 – 381

5

Missing in AAF87242. Ref.4

Sequence conflict

681

1

T → S in BAG63234. Ref.2

Secondary structure

1

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894

Helix Strand Turn

Details...

Helix

199 – 201

3

Beta strand

203 – 205

3

Turn

206 – 209

4

Beta strand

210 – 216

7

Turn

217 – 219

3

Helix

237 – 240

4

Beta strand

246 – 250

5

Beta strand

258 – 262

5

Beta strand

278 – 281

4

Helix

284 – 286

3

Beta strand

289 – 298

10

Beta strand

301 – 306

6

Turn

310 – 312

3

Helix

315 – 318

4

Turn

325 – 327

3

Beta strand

330 – 335

6

Beta strand

338 – 345

8

Beta strand

354 – 356

3

Helix

362 – 367

6

Turn

368 – 370

3

Helix

373 – 377

5

Beta strand

391 – 394

4

Beta strand

396 – 399

4

Helix

400 – 410

11

Sequences

	Sequence		Length	Mass (Da)
	Q9NQV7 [UniParc]. Last modified November 4, 2008. Version 2. Checksum: DE53094C32EFF83B	FASTA	894	103,376
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.

IPI

IPI00847313.

RefSeq

NP_064612.2. NM_020227.2.

UniGene

Hs.283096.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4IJD	X-ray	2.15	A/B	195-415	[»]

ProteinModelPortal

Q9NQV7.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000296682.

PTM databases

PhosphoSite

Q9NQV7.

Polymorphism databases

DMDM

212276459.

Proteomic databases

PaxDb

Q9NQV7.

PRIDE

Q9NQV7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000296682; ENSP00000296682; ENSG00000164256.

GeneID

56979.

KEGG

hsa:56979.

UCSC

uc003jgo.3. human.

Organism-specific databases

CTD

56979.

GeneCards

GC05P023558.

HGNC

HGNC:13994. PRDM9.

MIM

609760. gene.

neXtProt

NX_Q9NQV7.

PharmGKB

PA33721.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5048.

HOGENOM

HOG000234617.

HOVERGEN

HBG108291.

InParanoid

Q9NQV7.

OMA

RECGWGF.

OrthoDB

EOG4SF95W.

Enzyme and pathway databases

Reactome

REACT_111183. Meiosis.

Gene expression databases

ArrayExpress

Q9NQV7.

Bgee

Q9NQV7.

CleanEx

HS_PRDM9.

Genevestigator

Q9NQV7.

GermOnline

ENSG00000164256. Homo sapiens.

Family and domain databases

Gene3D

3.30.160.60. 13 hits.

InterPro

IPR001909. 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]

Pfam

PF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
[Graphical view]

SMART

SM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 14 hits.
[Graphical view]

SUPFAM

SSF109640. Krueppel-associated_box. 1 hit.

PROSITE

PS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 13 hits.
PS50157. ZINC_FINGER_C2H2_2. 14 hits.
[Graphical view]

ProtoNet

Search...

Other

GenomeRNAi

56979.

NextBio

62639.

SOURCE

Search...

Entry information

Entry name

PRDM9_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 103 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.