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Protein

PR domain zinc finger protein 1

Gene

PRDM1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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. 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 (By similarity). Binds specifically to the PRDI element in the promoter of the beta-interferon gene (PubMed:1851123). Drives the maturation of B-lymphocytes into Ig secreting cells (PubMed:12626569). Associates with the transcriptional repressor ZNF683 to chromatin at gene promoter regions (By similarity).By similarity2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri575 – 597C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri603 – 625C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri631 – 653C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri659 – 681C2H2-type 4PROSITE-ProRule annotationAdd BLAST23

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Methyltransferase, Repressor, Transferase
Biological processAdaptive immunity, Immunity, Innate immunity, Transcription, Transcription regulation
LigandMetal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-6804754 Regulation of TP53 Expression
SIGNORiO75626

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 1 (EC:2.1.1.-)
Alternative name(s):
BLIMP-1
Beta-interferon gene positive regulatory domain I-binding factor
PR domain-containing protein 1
Positive regulatory domain I-binding factor 1
Short name:
PRDI-BF1
Short name:
PRDI-binding factor 1
Gene namesi
Name:PRDM1
Synonyms:BLIMP1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000057657.14
HGNCiHGNC:9346 PRDM1
MIMi603423 gene
neXtProtiNX_O75626

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi639
OpenTargetsiENSG00000057657
PharmGKBiPA33707

Polymorphism and mutation databases

BioMutaiPRDM1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477571 – 825PR domain zinc finger protein 1Add BLAST825

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki816Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternate1 Publication
Cross-linki816Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources

Post-translational modificationi

Sumoylation at Lys-816 by PIAS1 augments transcriptional repressor activity, and is critical for plasma cell differentiation.1 Publication
Ubiquitinated by the SCF(FBXO11) complex, leading to its degradation by the proteasome.1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiO75626
PaxDbiO75626
PeptideAtlasiO75626
PRIDEiO75626
ProteomicsDBi50124
50125 [O75626-2]
50126 [O75626-3]

PTM databases

iPTMnetiO75626
PhosphoSitePlusiO75626

Expressioni

Gene expression databases

BgeeiENSG00000057657 Expressed in 179 organ(s), highest expression level in ectocervix
CleanExiHS_PRDM1
ExpressionAtlasiO75626 baseline and differential
GenevisibleiO75626 HS

Organism-specific databases

HPAiHPA030033

Interactioni

Subunit structurei

Interacts with PRMT5 (By similarity). Interacts with FBXO10 (PubMed:24613396). Interacts with FBXO11 (PubMed:24613396, PubMed:24968003).By similarity2 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi107108, 32 interactors
IntActiO75626, 7 interactors
MINTiO75626
STRINGi9606.ENSP00000358092

Structurei

Secondary structure

1825
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO75626
SMRiO75626
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO75626

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini84 – 201SETPROSITE-ProRule annotationAdd BLAST118

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni527 – 574Interaction with PIAS1Add BLAST48

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri575 – 597C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri603 – 625C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri631 – 653C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri659 – 681C2H2-type 4PROSITE-ProRule annotationAdd BLAST23

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG2461 Eukaryota
ENOG410ZFVU LUCA
GeneTreeiENSGT00880000137973
HOGENOMiHOG000059670
HOVERGENiHBG053670
InParanoidiO75626
OMAiKRNMTGY
OrthoDBiEOG091G0467
PhylomeDBiO75626
TreeFamiTF316545

Family and domain databases

InterProiView protein in InterPro
IPR001214 SET_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF00856 SET, 1 hit
PF00096 zf-C2H2, 2 hits
SMARTiView protein in SMART
SM00317 SET, 1 hit
SM00355 ZnF_C2H2, 5 hits
SUPFAMiSSF57667 SSF57667, 3 hits
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 4 hits
PS50157 ZINC_FINGER_C2H2_2, 4 hits

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: O75626-1) [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
MLDICLEKRV GTTLAAPKCN SSTVRFQGLA EGTKGTMKMD MEDADMTLWT
60 70 80 90 100
EAEFEEKCTY IVNDHPWDSG ADGGTSVQAE ASLPRNLLFK YATNSEEVIG
110 120 130 140 150
VMSKEYIPKG TRFGPLIGEI YTNDTVPKNA NRKYFWRIYS RGELHHFIDG
160 170 180 190 200
FNEEKSNWMR YVNPAHSPRE QNLAACQNGM NIYFYTIKPI PANQELLVWY
210 220 230 240 250
CRDFAERLHY PYPGELTMMN LTQTQSSLKQ PSTEKNELCP KNVPKREYSV
260 270 280 290 300
KEILKLDSNP SKGKDLYRSN ISPLTSEKDL DDFRRRGSPE MPFYPRVVYP
310 320 330 340 350
IRAPLPEDFL KASLAYGIER PTYITRSPIP SSTTPSPSAR SSPDQSLKSS
360 370 380 390 400
SPHSSPGNTV SPVGPGSQEH RDSYAYLNAS YGTEGLGSYP GYAPLPHLPP
410 420 430 440 450
AFIPSYNAHY PKFLLPPYGM NCNGLSAVSS MNGINNFGLF PRLCPVYSNL
460 470 480 490 500
LGGGSLPHPM LNPTSLPSSL PSDGARRLLQ PEHPREVLVP APHSAFSFTG
510 520 530 540 550
AAASMKDKAC SPTSGSPTAG TAATAEHVVQ PKATSAAMAA PSSDEAMNLI
560 570 580 590 600
KNKRNMTGYK TLPYPLKKQN GKIKYECNVC AKTFGQLSNL KVHLRVHSGE
610 620 630 640 650
RPFKCQTCNK GFTQLAHLQK HYLVHTGEKP HECQVCHKRF SSTSNLKTHL
660 670 680 690 700
RLHSGEKPYQ CKVCPAKFTQ FVHLKLHKRL HTRERPHKCS QCHKNYIHLC
710 720 730 740 750
SLKVHLKGNC AAAPAPGLPL EDLTRINEEI EKFDISDNAD RLEDVEDDIS
760 770 780 790 800
VISVVEKEIL AVVRKEKEET GLKVSLQRNM GNGLLSSGCS LYESSDLPLM
810 820
KLPPSNPLPL VPVKVKQETV EPMDP
Length:825
Mass (Da):91,771
Last modified:May 18, 2010 - v2
Checksum:i07B389BACCD6172F
GO
Isoform 2 (identifier: O75626-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.

Show »
Length:789
Mass (Da):87,991
Checksum:i6A1FEBEAD309BC7D
GO
Isoform 3 (identifier: O75626-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-3: MLD → MEK
     4-137: Missing.

Show »
Length:691
Mass (Da):76,835
Checksum:i4C5A56D19255FE89
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B2REA4B2REA4_HUMAN
PR domain zinc finger protein 1
PRDM1
171Annotation score:
B2REA5B2REA5_HUMAN
PR domain zinc finger protein 1
PRDM1
63Annotation score:

Sequence cautioni

The sequence AAO45623 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01998374G → S. Corresponds to variant dbSNP:rs2185379EnsemblClinVar.1
Natural variantiVAR_024221203D → E. Corresponds to variant dbSNP:rs811925EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0391881 – 36Missing in isoform 2. 1 PublicationAdd BLAST36
Alternative sequenceiVSP_0436461 – 3MLD → MEK in isoform 3. 2 Publications3
Alternative sequenceiVSP_0436474 – 137Missing in isoform 3. 2 PublicationsAdd BLAST134

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF084199 mRNA Translation: AAC33300.1
AY198414 mRNA Translation: AAO45623.1 Different initiation.
AY198415 mRNA Translation: AAO45624.1
AL358952 Genomic DNA No translation available.
AL022067 Genomic DNA No translation available.
CH471051 Genomic DNA Translation: EAW48419.1
CH471051 Genomic DNA Translation: EAW48421.1
CH471051 Genomic DNA Translation: EAW48422.1
BC103832 mRNA Translation: AAI03833.1
BC103833 mRNA Translation: AAI03834.1
BC103834 mRNA Translation: AAI03835.1
CCDSiCCDS34505.1 [O75626-3]
CCDS5054.2 [O75626-1]
PIRiA39564
RefSeqiNP_001189.2, NM_001198.3 [O75626-1]
NP_878911.1, NM_182907.2 [O75626-3]
XP_011534365.1, XM_011536063.2 [O75626-2]
XP_016866676.1, XM_017011187.1 [O75626-2]
UniGeneiHs.436023

Genome annotation databases

EnsembliENST00000369089; ENSP00000358085; ENSG00000057657 [O75626-3]
ENST00000369091; ENSP00000358087; ENSG00000057657 [O75626-2]
ENST00000369096; ENSP00000358092; ENSG00000057657 [O75626-1]
GeneIDi639
KEGGihsa:639
UCSCiuc003prd.3 human [O75626-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF084199 mRNA Translation: AAC33300.1
AY198414 mRNA Translation: AAO45623.1 Different initiation.
AY198415 mRNA Translation: AAO45624.1
AL358952 Genomic DNA No translation available.
AL022067 Genomic DNA No translation available.
CH471051 Genomic DNA Translation: EAW48419.1
CH471051 Genomic DNA Translation: EAW48421.1
CH471051 Genomic DNA Translation: EAW48422.1
BC103832 mRNA Translation: AAI03833.1
BC103833 mRNA Translation: AAI03834.1
BC103834 mRNA Translation: AAI03835.1
CCDSiCCDS34505.1 [O75626-3]
CCDS5054.2 [O75626-1]
PIRiA39564
RefSeqiNP_001189.2, NM_001198.3 [O75626-1]
NP_878911.1, NM_182907.2 [O75626-3]
XP_011534365.1, XM_011536063.2 [O75626-2]
XP_016866676.1, XM_017011187.1 [O75626-2]
UniGeneiHs.436023

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3DALX-ray1.65A/B38-223[»]
ProteinModelPortaliO75626
SMRiO75626
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107108, 32 interactors
IntActiO75626, 7 interactors
MINTiO75626
STRINGi9606.ENSP00000358092

PTM databases

iPTMnetiO75626
PhosphoSitePlusiO75626

Polymorphism and mutation databases

BioMutaiPRDM1

Proteomic databases

MaxQBiO75626
PaxDbiO75626
PeptideAtlasiO75626
PRIDEiO75626
ProteomicsDBi50124
50125 [O75626-2]
50126 [O75626-3]

Protocols and materials databases

DNASUi639
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369089; ENSP00000358085; ENSG00000057657 [O75626-3]
ENST00000369091; ENSP00000358087; ENSG00000057657 [O75626-2]
ENST00000369096; ENSP00000358092; ENSG00000057657 [O75626-1]
GeneIDi639
KEGGihsa:639
UCSCiuc003prd.3 human [O75626-1]

Organism-specific databases

CTDi639
DisGeNETi639
EuPathDBiHostDB:ENSG00000057657.14
GeneCardsiPRDM1
H-InvDBiHIX0006099
HGNCiHGNC:9346 PRDM1
HPAiHPA030033
MIMi603423 gene
neXtProtiNX_O75626
OpenTargetsiENSG00000057657
PharmGKBiPA33707
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2461 Eukaryota
ENOG410ZFVU LUCA
GeneTreeiENSGT00880000137973
HOGENOMiHOG000059670
HOVERGENiHBG053670
InParanoidiO75626
OMAiKRNMTGY
OrthoDBiEOG091G0467
PhylomeDBiO75626
TreeFamiTF316545

Enzyme and pathway databases

ReactomeiR-HSA-6804754 Regulation of TP53 Expression
SIGNORiO75626

Miscellaneous databases

ChiTaRSiPRDM1 human
EvolutionaryTraceiO75626
GeneWikiiPRDM1
GenomeRNAii639
PROiPR:O75626
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000057657 Expressed in 179 organ(s), highest expression level in ectocervix
CleanExiHS_PRDM1
ExpressionAtlasiO75626 baseline and differential
GenevisibleiO75626 HS

Family and domain databases

InterProiView protein in InterPro
IPR001214 SET_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF00856 SET, 1 hit
PF00096 zf-C2H2, 2 hits
SMARTiView protein in SMART
SM00317 SET, 1 hit
SM00355 ZnF_C2H2, 5 hits
SUPFAMiSSF57667 SSF57667, 3 hits
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 4 hits
PS50157 ZINC_FINGER_C2H2_2, 4 hits
ProtoNetiSearch...

Entry informationi

Entry nameiPRDM1_HUMAN
AccessioniPrimary (citable) accession number: O75626
Secondary accession number(s): B2REA6, E1P5E0, Q86WM7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: May 18, 2010
Last modified: October 10, 2018
This is version 168 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
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Main funding by: National Institutes of Health

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