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Protein

PR domain zinc finger protein 5

Gene

Prdm5

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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 (By similarity). May regulate the expression of proteins involved in extracellular matrix development and maintenance, connective tissue components and molecules regulating cell migration and adhesion. May caused G2/M arrest and apoptosis in cancer cells (By similarity).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri167 – 19024C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri199 – 22123C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri231 – 25626C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri264 – 28623C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri289 – 31123C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri317 – 33923C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri345 – 36723C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri373 – 39523C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri401 – 42424C2H2-type 9PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri430 – 45223C2H2-type 10PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri458 – 48023C2H2-type 11PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri486 – 50823C2H2-type 12PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri514 – 53623C2H2-type 13; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri542 – 56423C2H2-type 14PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri571 – 59424C2H2-type 15PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. methyltransferase activity Source: UniProtKB-KW
  3. repressing transcription factor binding Source: UniProtKB
  4. RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: MGI
  5. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Source: MGI
  6. sequence-specific DNA binding Source: UniProtKB
  7. transcription regulatory region DNA binding Source: UniProtKB

GO - Biological processi

  1. histone deacetylation Source: UniProtKB
  2. histone H3-K9 methylation Source: UniProtKB
  3. mitotic cell cycle Source: UniProtKB
  4. negative regulation of transcription, DNA-templated Source: UniProtKB
  5. negative regulation of transcription from RNA polymerase II promoter Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 5 (EC:2.1.1.-)
Alternative name(s):
PR domain-containing protein 5
Gene namesi
Name:Prdm5
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 6

Organism-specific databases

MGIiMGI:1918029. Prdm5.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 599599PR domain zinc finger protein 5PRO_0000230794Add
BLAST

Proteomic databases

PRIDEiQ9CXE0.

PTM databases

PhosphoSiteiQ9CXE0.

Expressioni

Gene expression databases

BgeeiQ9CXE0.
CleanExiMM_PRDM5.
ExpressionAtlasiQ9CXE0. baseline and differential.
GenevestigatoriQ9CXE0.

Interactioni

Subunit structurei

Interacts with EHMT2/G9A, GFI1 and HDAC1.By similarity

Protein-protein interaction databases

BioGridi214249. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ9CXE0.
SMRiQ9CXE0. Positions 9-589.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini8 – 124117SETPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi129 – 1346Poly-Glu

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 15 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri167 – 19024C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri199 – 22123C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri231 – 25626C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri264 – 28623C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri289 – 31123C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri317 – 33923C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri345 – 36723C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri373 – 39523C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri401 – 42424C2H2-type 9PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri430 – 45223C2H2-type 10PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri458 – 48023C2H2-type 11PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri486 – 50823C2H2-type 12PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri514 – 53623C2H2-type 13; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri542 – 56423C2H2-type 14PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri571 – 59424C2H2-type 15PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5048.
GeneTreeiENSGT00780000122027.
HOGENOMiHOG000234617.
HOVERGENiHBG098380.
InParanoidiQ9CXE0.
OMAiLGCKEDY.
OrthoDBiEOG7KSX7Q.
PhylomeDBiQ9CXE0.
TreeFamiTF106478.

Family and domain databases

Gene3Di3.30.160.60. 14 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR017125. Znf_PRDM5.
[Graphical view]
PfamiPF00096. zf-C2H2. 3 hits.
[Graphical view]
PIRSFiPIRSF037162. PRDM. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 15 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 15 hits.
PS50157. ZINC_FINGER_C2H2_2. 15 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9CXE0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLGMYVPDRF ALKSSRVQDG MGLYTARRVR KGEKFGPFAG EKRMPEDLDE
60 70 80 90 100
NMDYRLMWEV RGSKGEVLYI LDATNPRHSN WLRFVHEAPS QERKNLAAIQ
110 120 130 140 150
EGENIFYLAV DDIETDTELL IGYLDSDVEA EEEEQQALTM TKEGKVDHSK
160 170 180 190 200
GQLAAGSKGH LGCEEDFACP QCESSFPSEE VLTEHLQSLH QKPTGEKEFK
210 220 230 240 250
CENCGKKFPV RQALQRHFEQ HRKACRGEAR FVCKADSCGK RLKSKDALRR
260 270 280 290 300
HQENVHTGDP KRKLICSVCN RKCTSVSSLQ EHRKIHEIFD CQECMKKFIS
310 320 330 340 350
ANQLKRHMIT HSEKRPYNCE ICNKSFKRLD QVGAHKVIHS EDKPYQCKLC
360 370 380 390 400
GKGFAHRNVY KNHKKTHSEE RPFQCDACKA LFRTPFSLQR HLLIHNSERT
410 420 430 440 450
FKCHHCDATF KRKDTLNVHV QVVHERHKKY RCELCNKAFV TPSVLRSHKK
460 470 480 490 500
THTGEKEKVC PYCGQKFASS GTLRVHIRSH TGERPYQCPY CEKGFSKNDG
510 520 530 540 550
LKMHIRTHTR EKPYQCSECS KAFSQKRGLD EHKRTHTGEK PFQCDVCDLA
560 570 580 590
FSLKKMLIRH KMTHNPNRPM AECHFCHKKF TRNDYLKVHM DNIHGVADS
Length:599
Mass (Da):69,550
Last modified:July 7, 2009 - v2
Checksum:i545824C2A54DAAF6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti531 – 5322EH → AT in BAB29400 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK014501 mRNA. Translation: BAB29400.1.
CH466523 Genomic DNA. Translation: EDK98780.1.
BC138901 mRNA. Translation: AAI38902.1.
BC138902 mRNA. Translation: AAI38903.1.
CCDSiCCDS20208.1.
RefSeqiNP_081823.2. NM_027547.2.
UniGeneiMm.263355.

Genome annotation databases

EnsembliENSMUST00000031976; ENSMUSP00000031976; ENSMUSG00000029913.
GeneIDi70779.
KEGGimmu:70779.
UCSCiuc009cek.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK014501 mRNA. Translation: BAB29400.1.
CH466523 Genomic DNA. Translation: EDK98780.1.
BC138901 mRNA. Translation: AAI38902.1.
BC138902 mRNA. Translation: AAI38903.1.
CCDSiCCDS20208.1.
RefSeqiNP_081823.2. NM_027547.2.
UniGeneiMm.263355.

3D structure databases

ProteinModelPortaliQ9CXE0.
SMRiQ9CXE0. Positions 9-589.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi214249. 1 interaction.

PTM databases

PhosphoSiteiQ9CXE0.

Proteomic databases

PRIDEiQ9CXE0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000031976; ENSMUSP00000031976; ENSMUSG00000029913.
GeneIDi70779.
KEGGimmu:70779.
UCSCiuc009cek.1. mouse.

Organism-specific databases

CTDi11107.
MGIiMGI:1918029. Prdm5.

Phylogenomic databases

eggNOGiCOG5048.
GeneTreeiENSGT00780000122027.
HOGENOMiHOG000234617.
HOVERGENiHBG098380.
InParanoidiQ9CXE0.
OMAiLGCKEDY.
OrthoDBiEOG7KSX7Q.
PhylomeDBiQ9CXE0.
TreeFamiTF106478.

Miscellaneous databases

NextBioi332236.
PROiQ9CXE0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9CXE0.
CleanExiMM_PRDM5.
ExpressionAtlasiQ9CXE0. baseline and differential.
GenevestigatoriQ9CXE0.

Family and domain databases

Gene3Di3.30.160.60. 14 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR017125. Znf_PRDM5.
[Graphical view]
PfamiPF00096. zf-C2H2. 3 hits.
[Graphical view]
PIRSFiPIRSF037162. PRDM. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 15 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 15 hits.
PS50157. ZINC_FINGER_C2H2_2. 15 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Liver.
  2. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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].
    Tissue: Brain.

Entry informationi

Entry nameiPRDM5_MOUSE
AccessioniPrimary (citable) accession number: Q9CXE0
Secondary accession number(s): B2RSK8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: July 7, 2009
Last modified: March 4, 2015
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.