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O75626

- PRDM1_HUMAN

UniProt

O75626 - PRDM1_HUMAN

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Protein

PR domain zinc finger protein 1

Gene
PRDM1, BLIMP1
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri575 – 59723C2H2-type 1Add
BLAST
Zinc fingeri603 – 62523C2H2-type 2Add
BLAST
Zinc fingeri631 – 65323C2H2-type 3Add
BLAST
Zinc fingeri659 – 68123C2H2-type 4Add
BLAST

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. methyltransferase activity Source: UniProtKB-KW
  3. protein binding Source: IntAct
  4. sequence-specific DNA binding Source: Ensembl
  5. sequence-specific DNA binding transcription factor activity Source: ProtInc

GO - Biological processi

  1. cell fate commitment Source: Ensembl
  2. eye photoreceptor cell development Source: Ensembl
  3. germ cell development Source: Ensembl
  4. maternal placenta development Source: Ensembl
  5. negative regulation of B cell proliferation Source: Ensembl
  6. negative regulation of lipopolysaccharide-mediated signaling pathway Source: Ensembl
  7. negative regulation of transcription from RNA polymerase II promoter Source: ProtInc
  8. positive regulation of B cell differentiation Source: Ensembl
  9. positive regulation of gene expression Source: Ensembl
  10. transcription, DNA-templated Source: UniProtKB-KW
  11. trophoblast giant cell differentiation Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

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 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
ProteomesiUP000005640: Chromosome 6

Organism-specific databases

HGNCiHGNC:9346. PRDM1.

Subcellular locationi

Nucleus By similarity. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33707.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 825825PR domain zinc finger protein 1PRO_0000047757Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki816 – 816Glycyl 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

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiO75626.
PRIDEiO75626.

PTM databases

PhosphoSiteiO75626.

Expressioni

Gene expression databases

ArrayExpressiO75626.
BgeeiO75626.
CleanExiHS_PRDM1.
GenevestigatoriO75626.

Organism-specific databases

HPAiHPA030033.

Interactioni

Subunit structurei

Interacts with PRMT5 By similarity.

Binary interactionsi

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

Protein-protein interaction databases

BioGridi107108. 15 interactions.
IntActiO75626. 7 interactions.
MINTiMINT-2857156.
STRINGi9606.ENSP00000358092.

Structurei

Secondary structure

1
825
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi51 – 577
Beta strandi60 – 623
Helixi78 – 814
Beta strandi87 – 915
Beta strandi98 – 1058
Beta strandi111 – 1133
Beta strandi119 – 1213
Turni123 – 1253
Beta strandi135 – 1406
Beta strandi143 – 1497
Helixi158 – 1614
Turni168 – 1703
Beta strandi173 – 1786
Beta strandi181 – 1888
Beta strandi197 – 2004
Helixi202 – 2076
Helixi218 – 2225

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DALX-ray1.65A/B38-223[»]
ProteinModelPortaliO75626.
SMRiO75626. Positions 44-254, 525-705.

Miscellaneous databases

EvolutionaryTraceiO75626.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini84 – 201118SETAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni527 – 57448Interaction with PIAS1Add
BLAST

Sequence similaritiesi

Contains 1 SET domain.

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri575 – 59723C2H2-type 1Add
BLAST
Zinc fingeri603 – 62523C2H2-type 2Add
BLAST
Zinc fingeri631 – 65323C2H2-type 3Add
BLAST
Zinc fingeri659 – 68123C2H2-type 4Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5048.
HOGENOMiHOG000059670.
HOVERGENiHBG053670.
InParanoidiO75626.
OMAiTGYKTLP.
OrthoDBiEOG7060Q3.
PhylomeDBiO75626.
TreeFamiTF316545.

Family and domain databases

Gene3Di3.30.160.60. 5 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[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. Align

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

MLDICLEKRV GTTLAAPKCN SSTVRFQGLA EGTKGTMKMD MEDADMTLWT    50
EAEFEEKCTY IVNDHPWDSG ADGGTSVQAE ASLPRNLLFK YATNSEEVIG 100
VMSKEYIPKG TRFGPLIGEI YTNDTVPKNA NRKYFWRIYS RGELHHFIDG 150
FNEEKSNWMR YVNPAHSPRE QNLAACQNGM NIYFYTIKPI PANQELLVWY 200
CRDFAERLHY PYPGELTMMN LTQTQSSLKQ PSTEKNELCP KNVPKREYSV 250
KEILKLDSNP SKGKDLYRSN ISPLTSEKDL DDFRRRGSPE MPFYPRVVYP 300
IRAPLPEDFL KASLAYGIER PTYITRSPIP SSTTPSPSAR SSPDQSLKSS 350
SPHSSPGNTV SPVGPGSQEH RDSYAYLNAS YGTEGLGSYP GYAPLPHLPP 400
AFIPSYNAHY PKFLLPPYGM NCNGLSAVSS MNGINNFGLF PRLCPVYSNL 450
LGGGSLPHPM LNPTSLPSSL PSDGARRLLQ PEHPREVLVP APHSAFSFTG 500
AAASMKDKAC SPTSGSPTAG TAATAEHVVQ PKATSAAMAA PSSDEAMNLI 550
KNKRNMTGYK TLPYPLKKQN GKIKYECNVC AKTFGQLSNL KVHLRVHSGE 600
RPFKCQTCNK GFTQLAHLQK HYLVHTGEKP HECQVCHKRF SSTSNLKTHL 650
RLHSGEKPYQ CKVCPAKFTQ FVHLKLHKRL HTRERPHKCS QCHKNYIHLC 700
SLKVHLKGNC AAAPAPGLPL EDLTRINEEI EKFDISDNAD RLEDVEDDIS 750
VISVVEKEIL AVVRKEKEET GLKVSLQRNM GNGLLSSGCS LYESSDLPLM 800
KLPPSNPLPL VPVKVKQETV EPMDP 825
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 AAO45623.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti74 – 741G → S.
Corresponds to variant rs2185379 [ dbSNP | Ensembl ].
VAR_019983
Natural varianti203 – 2031D → E.
Corresponds to variant rs811925 [ dbSNP | Ensembl ].
VAR_024221

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 3636Missing in isoform 2. VSP_039188Add
BLAST
Alternative sequencei1 – 33MLD → MEK in isoform 3. VSP_043646
Alternative sequencei4 – 137134Missing in isoform 3. VSP_043647Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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]
UniGeneiHs.436023.

Genome annotation databases

EnsembliENST00000369089; ENSP00000358085; ENSG00000057657. [O75626-3]
ENST00000369091; ENSP00000358087; ENSG00000057657. [O75626-2]
ENST00000369096; ENSP00000358092; ENSG00000057657. [O75626-1]
GeneIDi639.
KEGGihsa:639.
UCSCiuc003prd.2. human. [O75626-1]
uc003pre.3. human. [O75626-3]

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:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS34505.1. [O75626-3 ]
CCDS5054.2. [O75626-1 ]
PIRi A39564.
RefSeqi NP_001189.2. NM_001198.3. [O75626-1 ]
NP_878911.1. NM_182907.2. [O75626-3 ]
UniGenei Hs.436023.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3DAL X-ray 1.65 A/B 38-223 [» ]
ProteinModelPortali O75626.
SMRi O75626. Positions 44-254, 525-705.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 107108. 15 interactions.
IntActi O75626. 7 interactions.
MINTi MINT-2857156.
STRINGi 9606.ENSP00000358092.

PTM databases

PhosphoSitei O75626.

Proteomic databases

PaxDbi O75626.
PRIDEi O75626.

Protocols and materials databases

DNASUi 639.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000369089 ; ENSP00000358085 ; ENSG00000057657 . [O75626-3 ]
ENST00000369091 ; ENSP00000358087 ; ENSG00000057657 . [O75626-2 ]
ENST00000369096 ; ENSP00000358092 ; ENSG00000057657 . [O75626-1 ]
GeneIDi 639.
KEGGi hsa:639.
UCSCi uc003prd.2. human. [O75626-1 ]
uc003pre.3. human. [O75626-3 ]

Organism-specific databases

CTDi 639.
GeneCardsi GC06P106534.
H-InvDB HIX0006099.
HGNCi HGNC:9346. PRDM1.
HPAi HPA030033.
MIMi 603423. gene.
neXtProti NX_O75626.
PharmGKBi PA33707.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG5048.
HOGENOMi HOG000059670.
HOVERGENi HBG053670.
InParanoidi O75626.
OMAi TGYKTLP.
OrthoDBi EOG7060Q3.
PhylomeDBi O75626.
TreeFami TF316545.

Miscellaneous databases

ChiTaRSi PRDM1. human.
EvolutionaryTracei O75626.
GeneWikii PRDM1.
GenomeRNAii 639.
NextBioi 2590.
PROi O75626.
SOURCEi Search...

Gene expression databases

ArrayExpressi O75626.
Bgeei O75626.
CleanExi HS_PRDM1.
Genevestigatori O75626.

Family and domain databases

Gene3Di 3.30.160.60. 5 hits.
InterProi IPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view ]
Pfami PF00856. SET. 1 hit.
[Graphical view ]
PIRSFi PIRSF013212. PRDM1. 1 hit.
SMARTi SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view ]
PROSITEi PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Identification and characterization of a novel repressor of beta-interferon gene expression."
    Keller A.D., Maniatis T.
    Genes Dev. 5:868-879(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  2. "Identification of a functionally impaired positive regulatory domain I binding factor 1 transcription repressor in myeloma cell lines."
    Gyory I., Fejer G., Ghosh N., Seto E., Wright K.L.
    J. Immunol. 170:3125-3133(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3).
  3. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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] (ISOFORM 3).
  6. "NANOS3 function in human germ cell development."
    Julaton V.T., Reijo Pera R.A.
    Hum. Mol. Genet. 20:2238-2250(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  7. "SUMOylation of Blimp-1 is critical for plasma cell differentiation."
    Ying H.Y., Su S.T., Hsu P.H., Chang C.C., Lin I.Y., Tseng Y.H., Tsai M.D., Shih H.M., Lin K.I.
    EMBO Rep. 13:631-637(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION AT LYS-816.
  8. "The crystal structure of methyltransferase domain of human PR domain-containing protein 1."
    Structural genomics consortium (SGC)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 38-223.

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: July 9, 2014
This is version 131 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

External Data

Dasty 3

Similar proteinsi