O75626 (PRDM1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
PR domain zinc finger protein 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	825 AA.
Sequence status	Complete.
Protein existence	Evidence 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	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 process	Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Repressor
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell fate commitment Inferred from electronic annotation. Source: Compara embryonic placenta development Inferred from electronic annotation. Source: Compara germ cell development Inferred from electronic annotation. Source: Compara maternal placenta development Inferred from electronic annotation. Source: Compara negative regulation of B cell proliferation Inferred from electronic annotation. Source: Compara negative regulation of lipopolysaccharide-mediated signaling pathway Inferred from electronic annotation. Source: Compara 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: Compara positive regulation of gene expression Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from direct assay Ref.6. Source: UniProtKB nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	sequence-specific DNA binding Inferred from electronic annotation. Source: Compara sequence-specific DNA binding transcription factor activity Traceable author statement Ref.1. Source: ProtInc zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 825

825

PR domain zinc finger protein 1

PRO_0000047757

Regions

Domain

85 – 205

121

SET

Zinc finger

575 – 597

23

C2H2-type 1

Zinc finger

603 – 625

23

C2H2-type 2

Zinc finger

631 – 653

23

C2H2-type 3

Zinc finger

659 – 681

23

C2H2-type 4

Region

527 – 574

48

Interaction with PIAS1

Amino acid modifications

Cross-link

816

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

Natural variations

Alternative sequence

1 – 36

36

Missing in isoform 2.

VSP_039188

Alternative sequence

1 – 3

3

MLD → MEK in isoform 3.

VSP_043646

Alternative sequence

4 – 137

134

Missing in isoform 3.

VSP_043647

Natural variant

74

1

G → S.
Corresponds to variant rs2185379 [ dbSNP | Ensembl ].

VAR_019983

Natural variant

203

1

D → E.
Corresponds to variant rs811925 [ dbSNP | Ensembl ].

VAR_024221

Secondary structure

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825

Helix Strand Turn

Details...

Helix

51 – 57

7

Beta strand

60 – 62

3

Helix

78 – 81

4

Beta strand

87 – 91

5

Beta strand

98 – 105

8

Beta strand

111 – 113

3

Beta strand

119 – 121

3

Turn

123 – 125

3

Beta strand

135 – 140

6

Beta strand

143 – 149

7

Helix

158 – 161

4

Turn

168 – 170

3

Beta strand

173 – 178

6

Beta strand

181 – 188

8

Beta strand

197 – 200

4

Helix

202 – 207

6

Helix

218 – 222

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 18, 2010. Version 2. Checksum: 07B389BACCD6172F	FASTA	825	91,771
	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
	Isoform 2 [UniParc]. Checksum: 6A1FEBEAD309BC7D	FASTA	789	87,991
	10 20 30 40 50 60 MKMDMEDADM TLWTEAEFEE KCTYIVNDHP WDSGADGGTS VQAEASLPRN LLFKYATNSE 70 80 90 100 110 120 EVIGVMSKEY IPKGTRFGPL IGEIYTNDTV PKNANRKYFW RIYSRGELHH FIDGFNEEKS 130 140 150 160 170 180 NWMRYVNPAH SPREQNLAAC QNGMNIYFYT IKPIPANQEL LVWYCRDFAE RLHYPYPGEL 190 200 210 220 230 240 TMMNLTQTQS SLKQPSTEKN ELCPKNVPKR EYSVKEILKL DSNPSKGKDL YRSNISPLTS 250 260 270 280 290 300 EKDLDDFRRR GSPEMPFYPR VVYPIRAPLP EDFLKASLAY GIERPTYITR SPIPSSTTPS 310 320 330 340 350 360 PSARSSPDQS LKSSSPHSSP GNTVSPVGPG SQEHRDSYAY LNASYGTEGL GSYPGYAPLP 370 380 390 400 410 420 HLPPAFIPSY NAHYPKFLLP PYGMNCNGLS AVSSMNGINN FGLFPRLCPV YSNLLGGGSL 430 440 450 460 470 480 PHPMLNPTSL PSSLPSDGAR RLLQPEHPRE VLVPAPHSAF SFTGAAASMK DKACSPTSGS 490 500 510 520 530 540 PTAGTAATAE HVVQPKATSA AMAAPSSDEA MNLIKNKRNM TGYKTLPYPL KKQNGKIKYE 550 560 570 580 590 600 CNVCAKTFGQ LSNLKVHLRV HSGERPFKCQ TCNKGFTQLA HLQKHYLVHT GEKPHECQVC 610 620 630 640 650 660 HKRFSSTSNL KTHLRLHSGE KPYQCKVCPA KFTQFVHLKL HKRLHTRERP HKCSQCHKNY 670 680 690 700 710 720 IHLCSLKVHL KGNCAAAPAP GLPLEDLTRI NEEIEKFDIS DNADRLEDVE DDISVISVVE 730 740 750 760 770 780 KEILAVVRKE KEETGLKVSL QRNMGNGLLS SGCSLYESSD LPLMKLPPSN PLPLVPVKVK QETVEPMDP
	Isoform 3 [UniParc]. Checksum: 4C5A56D19255FE89	FASTA	691	76,835
	10 20 30 40 50 60 MEKIYSRGEL HHFIDGFNEE KSNWMRYVNP AHSPREQNLA ACQNGMNIYF YTIKPIPANQ 70 80 90 100 110 120 ELLVWYCRDF AERLHYPYPG ELTMMNLTQT QSSLKQPSTE KNELCPKNVP KREYSVKEIL 130 140 150 160 170 180 KLDSNPSKGK DLYRSNISPL TSEKDLDDFR RRGSPEMPFY PRVVYPIRAP LPEDFLKASL 190 200 210 220 230 240 AYGIERPTYI TRSPIPSSTT PSPSARSSPD QSLKSSSPHS SPGNTVSPVG PGSQEHRDSY 250 260 270 280 290 300 AYLNASYGTE GLGSYPGYAP LPHLPPAFIP SYNAHYPKFL LPPYGMNCNG LSAVSSMNGI 310 320 330 340 350 360 NNFGLFPRLC PVYSNLLGGG SLPHPMLNPT SLPSSLPSDG ARRLLQPEHP REVLVPAPHS 370 380 390 400 410 420 AFSFTGAAAS MKDKACSPTS GSPTAGTAAT AEHVVQPKAT SAAMAAPSSD EAMNLIKNKR 430 440 450 460 470 480 NMTGYKTLPY PLKKQNGKIK YECNVCAKTF GQLSNLKVHL RVHSGERPFK CQTCNKGFTQ 490 500 510 520 530 540 LAHLQKHYLV HTGEKPHECQ VCHKRFSSTS NLKTHLRLHS GEKPYQCKVC PAKFTQFVHL 550 560 570 580 590 600 KLHKRLHTRE RPHKCSQCHK NYIHLCSLKV HLKGNCAAAP APGLPLEDLT RINEEIEKFD 610 620 630 640 650 660 ISDNADRLED VEDDISVISV VEKEILAVVR KEKEETGLKV SLQRNMGNGL LSSGCSLYES 670 680 690 SDLPLMKLPP SNPLPLVPVK VKQETVEPMD P

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.

IPI

IPI00385453.
IPI00747253.
IPI00915310.

PIR

A39564.

RefSeq

NP_001189.2. NM_001198.3.
NP_878911.1. NM_182907.2.

UniGene

Hs.436023.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3DAL	X-ray	1.65	A/B	38-223	[»]

ProteinModelPortal

O75626.

SMR

O75626. Positions 44-223, 525-707.

ModBase

Search...

Protein-protein interaction databases

IntAct

O75626. 4 interactions.

MINT

MINT-2857156.

STRING

9606.ENSP00000358092.

PTM databases

PhosphoSite

O75626.

Proteomic databases

PaxDb

O75626.

PRIDE

O75626.

Protocols and materials databases

DNASU

639.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000369089; ENSP00000358085; ENSG00000057657.
ENST00000369091; ENSP00000358087; ENSG00000057657.
ENST00000369096; ENSP00000358092; ENSG00000057657.

GeneID

639.

KEGG

hsa:639.

UCSC

uc003prd.2. human.

Organism-specific databases

CTD

639.

GeneCards

GC06P106579.

H-InvDB

HIX0006099.

HGNC

HGNC:9346. PRDM1.

HPA

HPA030033.

MIM

603423. gene.

neXtProt

NX_O75626.

PharmGKB

PA33707.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5048.

HOGENOM

HOG000059670.

HOVERGEN

HBG053670.

InParanoid

O75626.

OMA

KRNMTGY.

OrthoDB

EOG42821J.

Gene expression databases

ArrayExpress

O75626.

Bgee

O75626.

CleanEx

HS_PRDM1.

Genevestigator

O75626.

GermOnline

ENSG00000057657. Homo sapiens.

Family and domain databases

Gene3D

3.30.160.60. 5 hits.

InterPro

IPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view]

Pfam

PF00856. SET. 1 hit.
[Graphical view]

PIRSF

PIRSF013212. PRDM1. 1 hit.

SMART

SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view]

PROSITE

PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

PRDM1. human.

EvolutionaryTrace

O75626.

GenomeRNAi

639.

NextBio

2590.

SOURCE

Search...

Entry information

Entry name

PRDM1_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 119 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.