Q9NQX1 (PRDM5_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
PR domain zinc finger protein 5

Alternative name(s):
PR domain-containing protein 5

Gene names

Name:	PRDM5
Synonyms:	PFM2

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	630 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Sequence-specific DNA-binding transcription factor. Represses transcription at least in part by recruitment of the histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1. Regulates hematopoiesis-associated protein-coding and microRNA (miRNA) genes. May regulate the expression of proteins involved in extracellular matrix development and maintenance, including fibrillar collagens, such as COL4A1 and COL11A1, connective tissue components, such as HAPLN1, and molecules regulating cell migration and adhesion, including EDIL3 and TGFB2. May caused G2/M arrest and apoptosis in cancer cells. Ref.1 Ref.6 Ref.7
Subunit structure	Interacts with EHMT2/G9A, GFI1 and HDAC1. Ref.6
Subcellular location	Nucleus Ref.1 Ref.6.
Tissue specificity	Widely expressed with highest levels in colon and ovary. Tends to be silenced in breast, colorectal, gastric and liver cancer tissues. Ref.1 Ref.5
Involvement in disease	Brittle cornea syndrome 2 (BCS2) [MIM:614170]: A disorder characterized by extreme corneal thinning resulting in corneal rupture after minor trauma, blue sclerae, keratoconus or keratoglobus, hyperelasticity of the skin, and hypermobile joints. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.7
Sequence similarities	Contains 16 C2H2-type zinc fingers. Contains 1 SET domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Disease	Disease mutation
Domain	Repeat Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Activator Chromatin regulator Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone H3-K9 methylation Inferred from direct assay Ref.6. Source: UniProtKB histone deacetylation Inferred from mutant phenotype Ref.6. Source: UniProtKB mitotic cell cycle Inferred from mutant phenotype Ref.6. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from direct assay Ref.6. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from direct assay Ref.6. Source: UniProtKB
Molecular_function	repressing transcription factor binding Inferred from direct assay Ref.6. Source: UniProtKB sequence-specific DNA binding Inferred from direct assay Ref.6. Source: UniProtKB transcription regulatory region DNA binding Inferred from direct assay Ref.6. Source: UniProtKB transcription regulatory region sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EHMT2	Q96KQ7	3	EBI-4292031,EBI-744366
GFI1	Q99684	2	EBI-4292031,EBI-949368
HDAC1	Q13547	3	EBI-4292031,EBI-301834

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9NQX1-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q9NQX1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     218-248: Missing.

Isoform 3 (identifier: Q9NQX1-3)

The sequence of this isoform differs from the canonical sequence as follows:
     101-111: EGENIFYLAVE → DKNLGPAEWRG
     112-630: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 630	630	PR domain zinc finger protein 5		PRO_0000047761
Regions
	Domain	8 – 128	121	SET
	Zinc finger	167 – 190	24	C2H2-type 1
	Zinc finger	199 – 221	23	C2H2-type 2; atypical
	Zinc finger	234 – 256	23	C2H2-type 3; atypical
	Zinc finger	262 – 287	26	C2H2-type 4
	Zinc finger	295 – 317	23	C2H2-type 5
	Zinc finger	320 – 342	23	C2H2-type 6
	Zinc finger	348 – 370	23	C2H2-type 7
	Zinc finger	376 – 398	23	C2H2-type 8
	Zinc finger	404 – 426	23	C2H2-type 9
	Zinc finger	432 – 455	24	C2H2-type 10
	Zinc finger	461 – 483	23	C2H2-type 11
	Zinc finger	489 – 511	23	C2H2-type 12
	Zinc finger	517 – 539	23	C2H2-type 13
	Zinc finger	545 – 567	23	C2H2-type 14
	Zinc finger	573 – 595	23	C2H2-type 15
	Zinc finger	602 – 625	24	C2H2-type 16
Natural variations
	Alternative sequence	101 – 111	11	EGENIFYLAVE → DKNLGPAEWRG in isoform 3.		VSP_035652
	Alternative sequence	112 – 630	519	Missing in isoform 3.		VSP_035653
	Alternative sequence	218 – 248	31	Missing in isoform 2.		VSP_035654
	Natural variant	107	1	Y → C in BCS2. Ref.7		VAR_066393
Experimental info
	Sequence conflict	261	1	R → K in AAF78077. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 4, 2008. Version 2. Checksum: D16AF81AB5A34398	FASTA	630	73,090
	10 20 30 40 50 60 MLGMYVPDRF SLKSSRVQDG MGLYTARRVR KGEKFGPFAG EKRMPEDLDE NMDYRLMWEV 70 80 90 100 110 120 RGSKGEVLYI LDATNPRHSN WLRFVHEAPS QEQKNLAAIQ EGENIFYLAV EDIETDTELL 130 140 150 160 170 180 IGYLDSDMEA EEEEQQIMTV IKEGEVENSR RQSTAGRKDR LGCKEDYACP QCESSFTSED 190 200 210 220 230 240 ILAEHLQTLH QKPTEEKEFK CKNCGKKFPV KQALQRHVLQ CTAKSSLKES SRSFQCSVCN 250 260 270 280 290 300 SSFSSASSFE QHQETCRGDA RFVCKADSCG KRLKSKDALK RHQENVHTGD PKKKLICSVC 310 320 330 340 350 360 NKKCSSASSL QEHRKIHEIF DCQECMKKFI SANQLKRHMI THSEKRPYNC EICNKSFKRL 370 380 390 400 410 420 DQVGAHKVIH SEDKPYKCKL CGKGFAHRNV YKNHKKTHSE ERPFQCEECK ALFRTPFSLQ 430 440 450 460 470 480 RHLLIHNSER TFKCHHCDAT FKRKDTLNVH VQVVHERHKK YRCELCNKAF VTPSVLRSHK 490 500 510 520 530 540 KTHTGEKEKI CPYCGQKFAS SGTLRVHIRS HTGERPYQCP YCEKGFSKND GLKMHIRTHT 550 560 570 580 590 600 REKPYKCSEC SKAFSQKRGL DEHKRTHTGE KPFQCDVCDL AFSLKKMLIR HKMTHNPNRP 610 620 630 LAECQFCHKK FTRNDYLKVH MDNIHGVADS
	Isoform 2 [UniParc]. Checksum: 567E937469373B58	FASTA	599	69,862
	10 20 30 40 50 60 MLGMYVPDRF SLKSSRVQDG MGLYTARRVR KGEKFGPFAG EKRMPEDLDE NMDYRLMWEV 70 80 90 100 110 120 RGSKGEVLYI LDATNPRHSN WLRFVHEAPS QEQKNLAAIQ EGENIFYLAV EDIETDTELL 130 140 150 160 170 180 IGYLDSDMEA EEEEQQIMTV IKEGEVENSR RQSTAGRKDR LGCKEDYACP QCESSFTSED 190 200 210 220 230 240 ILAEHLQTLH QKPTEEKEFK CKNCGKKFPV KQALQRHFEQ HQETCRGDAR FVCKADSCGK 250 260 270 280 290 300 RLKSKDALKR HQENVHTGDP KKKLICSVCN KKCSSASSLQ EHRKIHEIFD CQECMKKFIS 310 320 330 340 350 360 ANQLKRHMIT HSEKRPYNCE ICNKSFKRLD QVGAHKVIHS EDKPYKCKLC GKGFAHRNVY 370 380 390 400 410 420 KNHKKTHSEE RPFQCEECKA LFRTPFSLQR HLLIHNSERT FKCHHCDATF KRKDTLNVHV 430 440 450 460 470 480 QVVHERHKKY RCELCNKAFV TPSVLRSHKK THTGEKEKIC PYCGQKFASS GTLRVHIRSH 490 500 510 520 530 540 TGERPYQCPY CEKGFSKNDG LKMHIRTHTR EKPYKCSECS KAFSQKRGLD EHKRTHTGEK 550 560 570 580 590 PFQCDVCDLA FSLKKMLIRH KMTHNPNRPL AECQFCHKKF TRNDYLKVHM DNIHGVADS
	Isoform 3 [UniParc]. Checksum: F0568A1C8495EC01	FASTA	111	12,874
	10 20 30 40 50 60 MLGMYVPDRF SLKSSRVQDG MGLYTARRVR KGEKFGPFAG EKRMPEDLDE NMDYRLMWEV 70 80 90 100 110 RGSKGEVLYI LDATNPRHSN WLRFVHEAPS QEQKNLAAIQ DKNLGPAEWR G

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PRDM5 is silenced in human cancers and has growth suppressive activities." Deng Q., Huang S. Oncogene 23:4903-4910(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[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] (ISOFORM 3).
[3]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3). Tissue: Brain.
[5]	"PRDM5 identified as a target of epigenetic silencing in colorectal and gastric cancer." Watanabe Y., Toyota M., Kondo Y., Suzuki H., Imai T., Ohe-Toyota M., Maruyama R., Nojima M., Sasaki Y., Sekido Y., Hiratsuka H., Shinomura Y., Imai K., Itoh F., Tokino T. Clin. Cancer Res. 13:4786-4794(2007) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY.
[6]	"Epigenetic regulation of protein-coding and microRNA genes by the Gfi1-interacting tumor suppressor PRDM5." Duan Z., Person R.E., Lee H.-H., Huang S., Donadieu J., Badolato R., Grimes H.L., Papayannopoulou T., Horwitz M.S. Mol. Cell. Biol. 27:6889-6902(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH EHMT2; GFI1 AND HDAC1, SUBCELLULAR LOCATION.
[7]	"Mutations in PRDM5 in brittle cornea syndrome identify a pathway regulating extracellular matrix development and maintenance." Burkitt Wright E.M., Spencer H.L., Daly S.B., Manson F.D., Zeef L.A., Urquhart J., Zoppi N., Bonshek R., Tosounidis I., Mohan M., Madden C., Dodds A., Chandler K.E., Banka S., Au L., Clayton-Smith J., Khan N., Biesecker L.G. , Wilson M., Rohrbach M., Colombi M., Giunta C., Black G.C. Am. J. Hum. Genet. 88:767-777(2011) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT BCS2 CYS-107, FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF272897 mRNA. Translation: AAF78077.1. AK056352 mRNA. Translation: BAG51686.1. AC025741 Genomic DNA. No translation available. AC104068 Genomic DNA. No translation available. AC104795 Genomic DNA. No translation available. BC066942 mRNA. Translation: AAH66942.1. BC121037 mRNA. Translation: AAI21038.1.
IPI	IPI00032997. IPI00744738. IPI00914659.
RefSeq	NP_061169.2. NM_018699.2.
UniGene	Hs.666782. Hs.669312.
3D structure databases
ProteinModelPortal	Q9NQX1.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9NQX1. 3 interactions.
STRING	9606.ENSP00000264808.
PTM databases
PhosphoSite	Q9NQX1.
Polymorphism databases
DMDM	212276458.
Proteomic databases
PaxDb	Q9NQX1.
PRIDE	Q9NQX1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000264808; ENSP00000264808; ENSG00000138738. ENST00000394435; ENSP00000377955; ENSG00000138738. ENST00000428209; ENSP00000404832; ENSG00000138738.
GeneID	11107.
KEGG	hsa:11107.
UCSC	uc003idn.3. human. uc003ido.3. human. uc003idp.1. human.
Organism-specific databases
CTD	11107.
GeneCards	GC04M121613.
HGNC	HGNC:9349. PRDM5.
HPA	HPA051406.
MIM	614161. gene. 614170. phenotype.
neXtProt	NX_Q9NQX1.
Orphanet	90354. Brittle cornea syndrome.
PharmGKB	PA33717.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG5048.
HOGENOM	HOG000234617.
HOVERGEN	HBG098380.
InParanoid	Q9NQX1.
OMA	LGCKEDY.
OrthoDB	EOG4R5027.
PhylomeDB	Q9NQX1.
Gene expression databases
ArrayExpress	Q9NQX1.
Bgee	Q9NQX1.
CleanEx	HS_PRDM5.
Genevestigator	Q9NQX1.
GermOnline	ENSG00000138738. Homo sapiens.
Family and domain databases
Gene3D	3.30.160.60. 14 hits.
InterPro	IPR001214. SET_dom. IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. IPR022755. Znf_C2H2_jaz. IPR017125. Znf_PRDM5. [Graphical view]
Pfam	PF00096. zf-C2H2. 2 hits. PF12171. zf-C2H2_jaz. 1 hit. [Graphical view]
PIRSF	PIRSF037162. PRDM. 1 hit.
SMART	SM00317. SET. 1 hit. SM00355. ZnF_C2H2. 16 hits. [Graphical view]
PROSITE	PS50280. SET. 1 hit. PS00028. ZINC_FINGER_C2H2_1. 14 hits. PS50157. ZINC_FINGER_C2H2_2. 16 hits. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	11107.
NextBio	42230.
SOURCE	Search...

Entry information

Entry name

PRDM5_HUMAN

Accession

Primary (citable) accession number: Q9NQX1
Secondary accession number(s): Q0VAJ0, Q6NXQ7

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 16, 2001
Last sequence update:	November 4, 2008
Last modified:	May 1, 2013
This is version 112 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.