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Protein

PR domain zinc finger protein 1

Gene

Prdm1

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

Functioni

Transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs (PubMed:27102484). Plays a role in the development, retention and long-term establishment of adaptive and innate tissue-resident lymphocyte T cell types in non-lymphoid organs, such as the skin and gut, but also in other nonbarrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection (PubMed:27102484). Binds specifically to the PRDI element in the promoter of the beta-interferon gene (By similarity). Drives the maturation of B-lymphocytes into Ig secreting cells (By similarity). Associates with the transcriptional repressor ZNF683 to chromatin at gene promoter regions (PubMed:27102484).By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri606 – 628C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri634 – 656C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri662 – 684C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri690 – 712C2H2-type 4PROSITE-ProRule annotationAdd BLAST23

GO - Molecular functioni

GO - Biological processi

  • adaptive immune response Source: UniProtKB-KW
  • aorta development Source: MGI
  • artery morphogenesis Source: MGI
  • cardiac septum development Source: MGI
  • cell fate commitment Source: MGI
  • coronary vasculature development Source: MGI
  • embryonic placenta development Source: MGI
  • eye photoreceptor cell development Source: MGI
  • germ cell development Source: MGI
  • heart valve development Source: MGI
  • innate immune response Source: UniProtKB-KW
  • intestinal epithelial cell development Source: MGI
  • in utero embryonic development Source: MGI
  • maternal placenta development Source: MGI
  • morphogenesis of a branching structure Source: MGI
  • negative regulation of B cell proliferation Source: MGI
  • negative regulation of gene expression Source: MGI
  • negative regulation of lipopolysaccharide-mediated signaling pathway Source: MGI
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • positive regulation of B cell differentiation Source: MGI
  • positive regulation of gene expression Source: MGI
  • post-embryonic development Source: MGI
  • regulation of cell proliferation Source: MGI
  • regulation of extrathymic T cell differentiation Source: UniProtKB
  • regulation of natural killer cell differentiation Source: UniProtKB
  • regulation of NK T cell differentiation Source: UniProtKB
  • sebum secreting cell proliferation Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • trophoblast giant cell differentiation Source: MGI
  • ventricular septum development Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Adaptive immunity, Immunity, Innate immunity, 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 1 (EC:2.1.1.-)
Alternative name(s):
B lymphocyte-induced maturation protein 1
Short name:
Blimp-1
Beta-interferon gene positive regulatory domain I-binding factor
PR domain-containing protein 1
Gene namesi
Name:Prdm1
Synonyms:Blimp1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:99655. Prdm1.

Subcellular locationi

  • Nucleus 1 Publication
  • Cytoplasm By similarity

GO - Cellular componenti

  • cytoplasm Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Early embryonic lethality (PubMed:19737919). Compound heterozygotes display germ cell defects and a rudimentary or missing fifth digit of the forelimb (PubMed:19737919). Conditional knockout in lymphocyte T cells show a weak reduction in tissue-resident memory T (Trm) cell population maintenance in the skin, gut, liver and kidney but not of splenic T cells (PubMed:27102484). Double knockouts for PRDM1/BLIMP1 and ZNF683 result in a strong inhibition of Trm cell population maintenance but not of circulating memory cells (PubMed:27102484). Display an enhancement of natural killer T (NKT) cells migration preferentially to the white pulp of the spleen in response to chemotactic stimuli (PubMed:27102484).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477581 – 856PR domain zinc finger protein 1Add BLAST856

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki847Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)By similarity

Post-translational modificationi

Sumoylation at Lys-847 by PIAS1 augments transcriptional repressor activity, and is critical for plasma cell differentiation.By similarity
Ubiquitinated by SCF(FBXO11), leading to its degradation by the proteasome.By similarity

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiQ60636.
PeptideAtlasiQ60636.
PRIDEiQ60636.

PTM databases

iPTMnetiQ60636.
PhosphoSitePlusiQ60636.

Expressioni

Tissue specificityi

Expressed in innate lymphocytes, including tissue-resident conventional natural killer (cNK) cells in liver (PubMed:27102484). Expressed also weakly in tissue-resident natural killer (trNK) and natural killer T (NKT) cells in liver (PubMed:27102484). Isoform 1 is detected in bone marrow, spleen and lymph node but not in brain, heart, kidney, liver, ovary or muscle. Weak expression detected in the lung. Isoform 3 is detected only in yolk sac. Isoform 4 is detected in embryo, yolk sac, placenta, splenocytes, and activated T-cells.4 Publications

Inductioni

By lymphokines, specifically IL-2 and IL-5. Up-regulated during dendritic cell maturation.
(Microbial infection) Up-regulated in response to Herpes simplex virus (HSV) infection in skin and spleen memory CD8+ T cells. Up-regulated in response to lymphocytic choriomeningitis virus (LCMV) in memory CD8+ T cells.1 Publication

Gene expression databases

BgeeiENSMUSG00000038151.
CleanExiMM_PRDM1.
GenevisibleiQ60636. MM.

Interactioni

Subunit structurei

Interacts with PRMT5 (PubMed:16699504). Interacts with FBXO10 (By similarity). Interacts with FBXO11 (By similarity).By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
SUMO1P631653EBI-7000804,EBI-80140From a different organism.

GO - Molecular functioni

  • histone deacetylase binding Source: MGI

Protein-protein interaction databases

BioGridi198355. 9 interactors.
IntActiQ60636. 1 interactor.
STRINGi10090.ENSMUSP00000101129.

Structurei

3D structure databases

ProteinModelPortaliQ60636.
SMRiQ60636.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini115 – 233SETPROSITE-ProRule annotationAdd BLAST119

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni558 – 605Interaction with PIAS1By similarityAdd BLAST48

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi351 – 394Glu/Pro/Ser/Thr-richAdd BLAST44

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri606 – 628C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri634 – 656C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri662 – 684C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri690 – 712C2H2-type 4PROSITE-ProRule annotationAdd BLAST23

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG2461. Eukaryota.
ENOG410ZFVU. LUCA.
GeneTreeiENSGT00830000128336.
HOGENOMiHOG000059670.
HOVERGENiHBG053670.
InParanoidiQ60636.
OMAiTGYKTLP.
OrthoDBiEOG091G0467.
PhylomeDBiQ60636.
TreeFamiTF316545.

Family and domain databases

Gene3Di3.30.160.60. 5 hits.
InterProiIPR016608. PRDM1.
IPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF13912. zf-C2H2_6. 2 hits.
[Graphical view]
PIRSFiPIRSF013212. PRDM1. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative promoter usage and alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q60636-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MREAYLRCWI FSWKNVWVRP CQRLHFKTVL LQGSLLYTAL DSYSTVQAAP
60 70 80 90 100
KSSSGSVKFQ GLAETGIMKM DMEDADMTLW TEAEFEEKCT YIVNDHPWDS
110 120 130 140 150
GADGGTSVQA EASLPRNLLF KYAANNSKEV IGVVSKEYIP KGTRFGPLIG
160 170 180 190 200
EVYTNDTVPK NANRKYFWRI YSREEFHHFI DGFNEEKSNW MRYVNPAHSA
210 220 230 240 250
REQNLAACQN GMNIYFYTIK PIPANQELLV WYCRDFAERL HYPYPGELTV
260 270 280 290 300
INLTQTESNP KQYSSEKNEL YPKSVPKREY SVKEILKLDS NPSKRKDIYR
310 320 330 340 350
SNISPFTLEK DMDGFRKNGS PDMPFYPRVV YPIRAPLPED FLKASLAYGM
360 370 380 390 400
ERPTYITHSP LPSSTTPSPP ASSSPEQSLK SSSPHSSPGN TVSPLAPGLP
410 420 430 440 450
EHRDSYSYLN VSYGSEGLGS YPGYAPAPHL PPAFIPSYNA HYPKFLLPPY
460 470 480 490 500
GISSNGLSTM NNINGINNFS LFPRLYPVYS NLLSGSSLPH PMLNPASLPS
510 520 530 540 550
SLPTDGARRL LPPEHPKEVL IPAPHSAFSL TGAAASMKDE SSPPSGSPTA
560 570 580 590 600
GTAATSEHVV QPKATSSVMA APSTDGAMNL IKNKRNMTGY KTLPYPLKKQ
610 620 630 640 650
NGKIKYECNV CAKTFGQLSN LKVHLRVHSG ERPFKCQTCN KGFTQLAHLQ
660 670 680 690 700
KHYLVHTGEK PHECQVCHKR FSSTSNLKTH LRLHSGEKPY QCKVCPAKFT
710 720 730 740 750
QFVHLKLHKR LHTRERPHKC AQCHKSYIHL CSLKVHLKGN CPAGPAAGLP
760 770 780 790 800
LEDLTRINEE IERFDISDNA DRLEDMEDSV DVTSMVEKEI LAVVRKEKEE
810 820 830 840 850
TSLKVSLQRN MGNGLLSSGC SLYESSDLSL MKLPHSNPLP LVPVKVKQET

VEPMDP
Note: Produced by alternative splicing.
Length:856
Mass (Da):95,836
Last modified:November 1, 1996 - v1
Checksum:iB9AC6FC2E29ECF4A
GO
Isoform 2 (identifier: Q60636-2) [UniParc]FASTAAdd to basket
Also known as: 1A

The sequence of this isoform differs from the canonical sequence as follows:
     1-47: MREAYLRCWIFSWKNVWVRPCQRLHFKTVLLQGSLLYTALDSYSTVQ → MLDLLLEKRVGTTL

Note: Produced by alternative splicing of isoform 1.
Show »
Length:823
Mass (Da):91,729
Checksum:i8B5904D42DDB2193
GO
Isoform 3 (identifier: Q60636-3) [UniParc]FASTAAdd to basket
Also known as: 1B

The sequence of this isoform differs from the canonical sequence as follows:
     1-67: Missing.

Note: Produced by alternative promoter usage of isoform 2.
Show »
Length:789
Mass (Da):88,228
Checksum:iD9C1AAA129A608C4
GO
Isoform 4 (identifier: Q60636-4) [UniParc]FASTAAdd to basket
Also known as: 1C

The sequence of this isoform differs from the canonical sequence as follows:
     1-47: MREAYLRCWI...TALDSYSTVQ → MTPGVPGHRTQQRPQHISALSDKAKDCSK

Note: Produced by alternative promoter usage of isoform 2.
Show »
Length:838
Mass (Da):93,302
Checksum:iEF258AECEFFB6B1A
GO
Isoform 5 (identifier: Q60636-5) [UniParc]FASTAAdd to basket
Also known as: delta exon 7

The sequence of this isoform differs from the canonical sequence as follows:
     624-666: Missing.

Note: Produced by alternative splicing of isoform 1. Does not bind DNA.
Show »
Length:813
Mass (Da):90,830
Checksum:iDDC40E049A8BE135
GO

Sequence cautioni

The sequence AAI29802 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti155N → K in AAI29802 (PubMed:15489334).Curated1
Sequence conflicti205L → M in AK077622 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0415701 – 67Missing in isoform 3. 1 PublicationAdd BLAST67
Alternative sequenceiVSP_0391891 – 47MREAY…YSTVQ → MLDLLLEKRVGTTL in isoform 2. 2 PublicationsAdd BLAST47
Alternative sequenceiVSP_0415711 – 47MREAY…YSTVQ → MTPGVPGHRTQQRPQHISAL SDKAKDCSK in isoform 4. CuratedAdd BLAST47
Alternative sequenceiVSP_041572624 – 666Missing in isoform 5. CuratedAdd BLAST43

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U08185 mRNA. Translation: AAA19252.1.
AF305539
, AF305534, AF305535, AF305536, AF305537, AF305538 Genomic DNA. Translation: AAG42212.1.
AK077622 mRNA. No translation available.
AK149344 mRNA. Translation: BAE28822.1.
BC129801 mRNA. Translation: AAI29802.1. Different initiation.
CCDSiCCDS23825.2. [Q60636-2]
PIRiA53503.
RefSeqiNP_031574.2. NM_007548.4. [Q60636-2]
XP_006512565.1. XM_006512502.3. [Q60636-4]
XP_006512566.1. XM_006512503.2. [Q60636-3]
XP_006512568.1. XM_006512505.2. [Q60636-1]
XP_011241411.1. XM_011243109.1. [Q60636-3]
UniGeneiMm.4800.

Genome annotation databases

EnsembliENSMUST00000039174; ENSMUSP00000039248; ENSMUSG00000038151. [Q60636-1]
ENSMUST00000105490; ENSMUSP00000101129; ENSMUSG00000038151. [Q60636-2]
GeneIDi12142.
KEGGimmu:12142.
UCSCiuc007ezu.3. mouse. [Q60636-1]
uc007ezv.3. mouse. [Q60636-2]

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U08185 mRNA. Translation: AAA19252.1.
AF305539
, AF305534, AF305535, AF305536, AF305537, AF305538 Genomic DNA. Translation: AAG42212.1.
AK077622 mRNA. No translation available.
AK149344 mRNA. Translation: BAE28822.1.
BC129801 mRNA. Translation: AAI29802.1. Different initiation.
CCDSiCCDS23825.2. [Q60636-2]
PIRiA53503.
RefSeqiNP_031574.2. NM_007548.4. [Q60636-2]
XP_006512565.1. XM_006512502.3. [Q60636-4]
XP_006512566.1. XM_006512503.2. [Q60636-3]
XP_006512568.1. XM_006512505.2. [Q60636-1]
XP_011241411.1. XM_011243109.1. [Q60636-3]
UniGeneiMm.4800.

3D structure databases

ProteinModelPortaliQ60636.
SMRiQ60636.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi198355. 9 interactors.
IntActiQ60636. 1 interactor.
STRINGi10090.ENSMUSP00000101129.

PTM databases

iPTMnetiQ60636.
PhosphoSitePlusiQ60636.

Proteomic databases

PaxDbiQ60636.
PeptideAtlasiQ60636.
PRIDEiQ60636.

Protocols and materials databases

DNASUi12142.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000039174; ENSMUSP00000039248; ENSMUSG00000038151. [Q60636-1]
ENSMUST00000105490; ENSMUSP00000101129; ENSMUSG00000038151. [Q60636-2]
GeneIDi12142.
KEGGimmu:12142.
UCSCiuc007ezu.3. mouse. [Q60636-1]
uc007ezv.3. mouse. [Q60636-2]

Organism-specific databases

CTDi639.
MGIiMGI:99655. Prdm1.

Phylogenomic databases

eggNOGiKOG2461. Eukaryota.
ENOG410ZFVU. LUCA.
GeneTreeiENSGT00830000128336.
HOGENOMiHOG000059670.
HOVERGENiHBG053670.
InParanoidiQ60636.
OMAiTGYKTLP.
OrthoDBiEOG091G0467.
PhylomeDBiQ60636.
TreeFamiTF316545.

Miscellaneous databases

PROiQ60636.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000038151.
CleanExiMM_PRDM1.
GenevisibleiQ60636. MM.

Family and domain databases

Gene3Di3.30.160.60. 5 hits.
InterProiIPR016608. PRDM1.
IPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF13912. zf-C2H2_6. 2 hits.
[Graphical view]
PIRSFiPIRSF013212. PRDM1. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRDM1_MOUSE
AccessioniPrimary (citable) accession number: Q60636
Secondary accession number(s): A2VDE8, Q3UET9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 147 of the entry and version 1 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

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 one 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.