Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

PR domain zinc finger protein 1

Gene

PRDM1

Organism
Homo sapiens (Human)
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. 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

Complete GO annotation...

Keywords - Molecular functioni

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000057657-MONOMER.
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

HGNCiHGNC:9346. PRDM1.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleoplasm Source: Reactome
Complete GO annotation...

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)1 Publication

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.

PTM databases

iPTMnetiO75626.
PhosphoSitePlusiO75626.

Expressioni

Gene expression databases

BgeeiENSG00000057657.
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

WithEntry#Exp.IntActNotes
PIAS1O759252EBI-948789,EBI-629434
SUMO1P631652EBI-7839538,EBI-80140

Protein-protein interaction databases

BioGridi107108. 31 interactors.
IntActiO75626. 7 interactors.
MINTiMINT-2857156.
STRINGi9606.ENSP00000358092.

Structurei

Secondary structure

1825
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi51 – 57Combined sources7
Beta strandi60 – 62Combined sources3
Helixi78 – 81Combined sources4
Beta strandi87 – 91Combined sources5
Beta strandi98 – 105Combined sources8
Beta strandi111 – 113Combined sources3
Beta strandi119 – 121Combined sources3
Turni123 – 125Combined sources3
Beta strandi135 – 140Combined sources6
Beta strandi143 – 149Combined sources7
Helixi158 – 161Combined sources4
Turni168 – 170Combined sources3
Beta strandi173 – 178Combined sources6
Beta strandi181 – 188Combined sources8
Beta strandi197 – 200Combined sources4
Helixi202 – 207Combined sources6
Helixi218 – 222Combined sources5

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...

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
Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.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.
GeneTreeiENSGT00830000128336.
HOGENOMiHOG000059670.
HOVERGENiHBG053670.
InParanoidiO75626.
OMAiTGYKTLP.
OrthoDBiEOG091G0467.
PhylomeDBiO75626.
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 (3)i

Sequence statusi: Complete.

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

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

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 rs2185379dbSNPEnsembl.1
Natural variantiVAR_024221203D → E.Corresponds to variant rs811925dbSNPEnsembl.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, AL022067 Genomic DNA. Translation: CAQ52574.1.
AL022067 Genomic DNA. Translation: CAI42295.2.
AL022067, AL358952 Genomic DNA. Translation: CAQ52608.1.
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

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, AL022067 Genomic DNA. Translation: CAQ52574.1.
AL022067 Genomic DNA. Translation: CAI42295.2.
AL022067, AL358952 Genomic DNA. Translation: CAQ52608.1.
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. 31 interactors.
IntActiO75626. 7 interactors.
MINTiMINT-2857156.
STRINGi9606.ENSP00000358092.

PTM databases

iPTMnetiO75626.
PhosphoSitePlusiO75626.

Polymorphism and mutation databases

BioMutaiPRDM1.

Proteomic databases

MaxQBiO75626.
PaxDbiO75626.
PeptideAtlasiO75626.
PRIDEiO75626.

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.
GeneCardsiPRDM1.
H-InvDBHIX0006099.
HGNCiHGNC:9346. PRDM1.
HPAiHPA030033.
MIMi603423. gene.
neXtProtiNX_O75626.
OpenTargetsiENSG00000057657.
PharmGKBiPA33707.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2461. Eukaryota.
ENOG410ZFVU. LUCA.
GeneTreeiENSGT00830000128336.
HOGENOMiHOG000059670.
HOVERGENiHBG053670.
InParanoidiO75626.
OMAiTGYKTLP.
OrthoDBiEOG091G0467.
PhylomeDBiO75626.
TreeFamiTF316545.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000057657-MONOMER.
ReactomeiR-HSA-6804754. Regulation of TP53 Expression.
SIGNORiO75626.

Miscellaneous databases

ChiTaRSiPRDM1. human.
EvolutionaryTraceiO75626.
GeneWikiiPRDM1.
GenomeRNAii639.
PROiO75626.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000057657.
CleanExiHS_PRDM1.
ExpressionAtlasiO75626. baseline and differential.
GenevisibleiO75626. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: O75626
Secondary accession number(s): B2REA6, E1P5E0, Q86WM7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: May 18, 2010
Last modified: November 2, 2016
This is version 152 of the entry and version 2 of the sequence. [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. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.