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Q9NQX1 (PRDM5_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 119. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
PR domain zinc finger protein 5

EC=2.1.1.-
Alternative name(s):
PR domain-containing protein 5
Gene names
Name:PRDM5
Synonyms:PFM2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length630 AA.
Sequence statusComplete.
Protein existenceEvidence 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

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

Contains 16 C2H2-type zinc fingers.

Contains 1 SET domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DiseaseDisease mutation
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Metal-binding
S-adenosyl-L-methionine
Zinc
   Molecular functionActivator
Chromatin regulator
Methyltransferase
Repressor
Transferase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processhistone 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-templated

Inferred from direct assay Ref.6. Source: UniProtKB

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay Ref.6. Source: UniProtKB

   Molecular_functionmetal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

methyltransferase activity

Inferred from electronic annotation. Source: UniProtKB-KW

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

Complete GO annotation...

Binary interactions

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 630630PR domain zinc finger protein 5
PRO_0000047761

Regions

Domain8 – 124117SET
Zinc finger167 – 19024C2H2-type 1
Zinc finger199 – 22123C2H2-type 2; atypical
Zinc finger234 – 25623C2H2-type 3; atypical
Zinc finger262 – 28726C2H2-type 4
Zinc finger295 – 31723C2H2-type 5
Zinc finger320 – 34223C2H2-type 6
Zinc finger348 – 37023C2H2-type 7
Zinc finger376 – 39823C2H2-type 8
Zinc finger404 – 42623C2H2-type 9
Zinc finger432 – 45524C2H2-type 10
Zinc finger461 – 48323C2H2-type 11
Zinc finger489 – 51123C2H2-type 12
Zinc finger517 – 53923C2H2-type 13
Zinc finger545 – 56723C2H2-type 14
Zinc finger573 – 59523C2H2-type 15
Zinc finger602 – 62524C2H2-type 16

Natural variations

Alternative sequence101 – 11111EGENIFYLAVE → DKNLGPAEWRG in isoform 3.
VSP_035652
Alternative sequence112 – 630519Missing in isoform 3.
VSP_035653
Alternative sequence218 – 24831Missing in isoform 2.
VSP_035654
Natural variant1071Y → C in BCS2. Ref.7
VAR_066393

Experimental info

Sequence conflict2611R → K in AAF78077. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 4, 2008. Version 2.
Checksum: D16AF81AB5A34398

FASTA63073,090
        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 

« Hide

Isoform 2 [UniParc].

Checksum: 567E937469373B58
Show »

FASTA59969,862
Isoform 3 [UniParc].

Checksum: F0568A1C8495EC01
Show »

FASTA11112,874

References

« Hide '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. 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] (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. expand/collapse author list , 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. expand/collapse author list , 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.
RefSeqNP_061169.2. NM_018699.2.
XP_005262763.1. XM_005262706.1.
UniGeneHs.666782.
Hs.669312.

3D structure databases

ProteinModelPortalQ9NQX1.
SMRQ9NQX1. Positions 4-620.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116287. 3 interactions.
IntActQ9NQX1. 3 interactions.
STRING9606.ENSP00000264808.

PTM databases

PhosphoSiteQ9NQX1.

Polymorphism databases

DMDM212276458.

Proteomic databases

PaxDbQ9NQX1.
PRIDEQ9NQX1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000264808; ENSP00000264808; ENSG00000138738. [Q9NQX1-1]
ENST00000394435; ENSP00000377955; ENSG00000138738. [Q9NQX1-3]
ENST00000428209; ENSP00000404832; ENSG00000138738. [Q9NQX1-2]
GeneID11107.
KEGGhsa:11107.
UCSCuc003idn.3. human. [Q9NQX1-1]
uc003ido.3. human. [Q9NQX1-2]
uc003idp.1. human. [Q9NQX1-3]

Organism-specific databases

CTD11107.
GeneCardsGC04M121613.
HGNCHGNC:9349. PRDM5.
HPAHPA051406.
MIM614161. gene.
614170. phenotype.
neXtProtNX_Q9NQX1.
Orphanet90354. Brittle cornea syndrome.
PharmGKBPA33717.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5048.
HOGENOMHOG000234617.
HOVERGENHBG098380.
InParanoidQ9NQX1.
OMALGCKEDY.
OrthoDBEOG7KSX7Q.
PhylomeDBQ9NQX1.
TreeFamTF106478.

Gene expression databases

ArrayExpressQ9NQX1.
BgeeQ9NQX1.
CleanExHS_PRDM5.
GenevestigatorQ9NQX1.

Family and domain databases

Gene3D3.30.160.60. 14 hits.
InterProIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR022755. Znf_C2H2_jaz.
IPR017125. Znf_PRDM5.
[Graphical view]
PfamPF00096. zf-C2H2. 3 hits.
PF12171. zf-C2H2_jaz. 1 hit.
[Graphical view]
PIRSFPIRSF037162. PRDM. 1 hit.
SMARTSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 16 hits.
[Graphical view]
PROSITEPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 14 hits.
PS50157. ZINC_FINGER_C2H2_2. 16 hits.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi11107.
NextBio42230.
PROQ9NQX1.
SOURCESearch...

Entry information

Entry namePRDM5_HUMAN
AccessionPrimary (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: March 19, 2014
This is version 119 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

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 4

Human chromosome 4: entries, gene names and cross-references to MIM