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O75626 (PRDM1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:PRDM1
Synonyms:BLIMP1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length825 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

Interacts with PRMT5 By similarity.

Subcellular location

Nucleus By similarity. Cytoplasm Ref.6.

Post-translational modification

Sumoylation at Lys-816 by PIAS1 augments transcriptional repressor activity, and is critical for plasma cell differentiation. Ref.7

Sequence similarities

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

Contains 4 C2H2-type zinc fingers.

Contains 1 SET domain.

Sequence caution

The sequence AAO45623.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Metal-binding
S-adenosyl-L-methionine
Zinc
   Molecular functionMethyltransferase
Repressor
Transferase
   PTMIsopeptide bond
Ubl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcell fate commitment

Inferred from electronic annotation. Source: Ensembl

eye photoreceptor cell development

Inferred from electronic annotation. Source: Ensembl

germ cell development

Inferred from electronic annotation. Source: Ensembl

maternal placenta development

Inferred from electronic annotation. Source: Ensembl

negative regulation of B cell proliferation

Inferred from electronic annotation. Source: Ensembl

negative regulation of lipopolysaccharide-mediated signaling pathway

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Traceable author statement Ref.1. Source: ProtInc

positive regulation of B cell differentiation

Inferred from electronic annotation. Source: Ensembl

positive regulation of gene expression

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

trophoblast giant cell differentiation

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentcytoplasm

Inferred from direct assay Ref.6. Source: UniProtKB

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionmetal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

methyltransferase activity

Inferred from electronic annotation. Source: UniProtKB-KW

sequence-specific DNA binding

Inferred from electronic annotation. Source: Ensembl

sequence-specific DNA binding transcription factor activity

Traceable author statement Ref.1. Source: ProtInc

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PIAS1O759252EBI-948789,EBI-629434
SUMO1P631652EBI-7839538,EBI-80140

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O75626-1)

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.
Isoform 2 (identifier: O75626-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.
Isoform 3 (identifier: O75626-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 825825PR domain zinc finger protein 1
PRO_0000047757

Regions

Domain84 – 201118SET
Zinc finger575 – 59723C2H2-type 1
Zinc finger603 – 62523C2H2-type 2
Zinc finger631 – 65323C2H2-type 3
Zinc finger659 – 68123C2H2-type 4
Region527 – 57448Interaction with PIAS1

Amino acid modifications

Cross-link816Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1) Ref.7

Natural variations

Alternative sequence1 – 3636Missing in isoform 2.
VSP_039188
Alternative sequence1 – 33MLD → MEK in isoform 3.
VSP_043646
Alternative sequence4 – 137134Missing in isoform 3.
VSP_043647
Natural variant741G → S.
Corresponds to variant rs2185379 [ dbSNP | Ensembl ].
VAR_019983
Natural variant2031D → E.
Corresponds to variant rs811925 [ dbSNP | Ensembl ].
VAR_024221

Secondary structure

................................... 825
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 18, 2010. Version 2.
Checksum: 07B389BACCD6172F

FASTA82591,771
        10         20         30         40         50         60 
MLDICLEKRV GTTLAAPKCN SSTVRFQGLA EGTKGTMKMD MEDADMTLWT EAEFEEKCTY 

        70         80         90        100        110        120 
IVNDHPWDSG ADGGTSVQAE ASLPRNLLFK YATNSEEVIG VMSKEYIPKG TRFGPLIGEI 

       130        140        150        160        170        180 
YTNDTVPKNA NRKYFWRIYS RGELHHFIDG FNEEKSNWMR YVNPAHSPRE QNLAACQNGM 

       190        200        210        220        230        240 
NIYFYTIKPI PANQELLVWY CRDFAERLHY PYPGELTMMN LTQTQSSLKQ PSTEKNELCP 

       250        260        270        280        290        300 
KNVPKREYSV KEILKLDSNP SKGKDLYRSN ISPLTSEKDL DDFRRRGSPE MPFYPRVVYP 

       310        320        330        340        350        360 
IRAPLPEDFL KASLAYGIER PTYITRSPIP SSTTPSPSAR SSPDQSLKSS SPHSSPGNTV 

       370        380        390        400        410        420 
SPVGPGSQEH RDSYAYLNAS YGTEGLGSYP GYAPLPHLPP AFIPSYNAHY PKFLLPPYGM 

       430        440        450        460        470        480 
NCNGLSAVSS MNGINNFGLF PRLCPVYSNL LGGGSLPHPM LNPTSLPSSL PSDGARRLLQ 

       490        500        510        520        530        540 
PEHPREVLVP APHSAFSFTG AAASMKDKAC SPTSGSPTAG TAATAEHVVQ PKATSAAMAA 

       550        560        570        580        590        600 
PSSDEAMNLI KNKRNMTGYK TLPYPLKKQN GKIKYECNVC AKTFGQLSNL KVHLRVHSGE 

       610        620        630        640        650        660 
RPFKCQTCNK GFTQLAHLQK HYLVHTGEKP HECQVCHKRF SSTSNLKTHL RLHSGEKPYQ 

       670        680        690        700        710        720 
CKVCPAKFTQ FVHLKLHKRL HTRERPHKCS QCHKNYIHLC SLKVHLKGNC AAAPAPGLPL 

       730        740        750        760        770        780 
EDLTRINEEI EKFDISDNAD RLEDVEDDIS VISVVEKEIL AVVRKEKEET GLKVSLQRNM 

       790        800        810        820 
GNGLLSSGCS LYESSDLPLM KLPPSNPLPL VPVKVKQETV EPMDP 

« Hide

Isoform 2 [UniParc].

Checksum: 6A1FEBEAD309BC7D
Show »

FASTA78987,991
Isoform 3 [UniParc].

Checksum: 4C5A56D19255FE89
Show »

FASTA69176,835

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA39564.
RefSeqNP_001189.2. NM_001198.3.
NP_878911.1. NM_182907.2.
UniGeneHs.436023.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3DALX-ray1.65A/B38-223[»]
ProteinModelPortalO75626.
SMRO75626. Positions 44-254, 525-705.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid107108. 15 interactions.
IntActO75626. 7 interactions.
MINTMINT-2857156.
STRING9606.ENSP00000358092.

PTM databases

PhosphoSiteO75626.

Proteomic databases

PaxDbO75626.
PRIDEO75626.

Protocols and materials databases

DNASU639.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000369089; ENSP00000358085; ENSG00000057657. [O75626-3]
ENST00000369091; ENSP00000358087; ENSG00000057657. [O75626-2]
ENST00000369096; ENSP00000358092; ENSG00000057657. [O75626-1]
GeneID639.
KEGGhsa:639.
UCSCuc003prd.2. human. [O75626-1]
uc003pre.3. human. [O75626-3]

Organism-specific databases

CTD639.
GeneCardsGC06P106534.
H-InvDBHIX0006099.
HGNCHGNC:9346. PRDM1.
HPAHPA030033.
MIM603423. gene.
neXtProtNX_O75626.
PharmGKBPA33707.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5048.
HOGENOMHOG000059670.
HOVERGENHBG053670.
InParanoidO75626.
OMATGYKTLP.
OrthoDBEOG7060Q3.
PhylomeDBO75626.
TreeFamTF316545.

Gene expression databases

ArrayExpressO75626.
BgeeO75626.
CleanExHS_PRDM1.
GenevestigatorO75626.

Family and domain databases

Gene3D3.30.160.60. 5 hits.
InterProIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view]
PfamPF00856. SET. 1 hit.
[Graphical view]
PIRSFPIRSF013212. PRDM1. 1 hit.
SMARTSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPRDM1. human.
EvolutionaryTraceO75626.
GeneWikiPRDM1.
GenomeRNAi639.
NextBio2590.
PROO75626.
SOURCESearch...

Entry information

Entry namePRDM1_HUMAN
AccessionPrimary (citable) accession number: O75626
Secondary accession number(s): B2REA6, E1P5E0, Q86WM7
Entry history
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: May 18, 2010
Last modified: April 16, 2014
This is version 128 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM