PRDM4_HUMAN
ID PRDM4_HUMAN Reviewed; 801 AA.
AC Q9UKN5; Q9UFA6;
DT 16-NOV-2001, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2002, sequence version 3.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=PR domain zinc finger protein 4;
DE EC=2.1.1.-;
DE AltName: Full=PR domain-containing protein 4;
GN Name=PRDM4; Synonyms=PFM1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=10552934; DOI=10.1006/geno.1999.5967;
RA Yang X.-H., Huang S.;
RT "PFM1 (PRDM4), a new member of the PR-domain family, maps to a tumor
RT suppressor locus on human chromosome 12q23-q24.1.";
RL Genomics 61:319-325(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 77-801.
RC TISSUE=Testis;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 390-540.
RG Structural genomics consortium (SGC);
RT "The crystal structure of methyltransferase domain of human PR domain-
RT containing protein 4.";
RL Submitted (AUG-2008) to the PDB data bank.
CC -!- FUNCTION: May function as a transcription factor involved in cell
CC differentiation.
CC -!- INTERACTION:
CC Q9UKN5; Q8WYA6: CTNNBL1; NbExp=3; IntAct=EBI-2803427, EBI-748128;
CC Q9UKN5; Q8IXL7: MSRB3; NbExp=3; IntAct=EBI-2803427, EBI-8634060;
CC Q9UKN5; P62166: NCS1; NbExp=3; IntAct=EBI-2803427, EBI-746987;
CC Q9UKN5; P46934: NEDD4; NbExp=2; IntAct=EBI-2803427, EBI-726944;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in many tissues. Highly expressed in
CC ovary, testis, pancreas, brain, heart and prostate.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
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DR EMBL; AF144757; AAD55249.2; -; mRNA.
DR EMBL; BC035581; AAH35581.1; -; mRNA.
DR EMBL; AL133083; CAB61401.1; -; mRNA.
DR CCDS; CCDS9115.1; -.
DR PIR; T42688; T42688.
DR RefSeq; NP_036538.3; NM_012406.3.
DR PDB; 2L9Z; NMR; -; A=366-402.
DR PDB; 3DB5; X-ray; 2.15 A; A/B=390-540.
DR PDBsum; 2L9Z; -.
DR PDBsum; 3DB5; -.
DR AlphaFoldDB; Q9UKN5; -.
DR BMRB; Q9UKN5; -.
DR SMR; Q9UKN5; -.
DR BioGRID; 116288; 19.
DR IntAct; Q9UKN5; 18.
DR MINT; Q9UKN5; -.
DR STRING; 9606.ENSP00000228437; -.
DR iPTMnet; Q9UKN5; -.
DR PhosphoSitePlus; Q9UKN5; -.
DR BioMuta; PRDM4; -.
DR DMDM; 25008960; -.
DR EPD; Q9UKN5; -.
DR jPOST; Q9UKN5; -.
DR MassIVE; Q9UKN5; -.
DR MaxQB; Q9UKN5; -.
DR PaxDb; Q9UKN5; -.
DR PeptideAtlas; Q9UKN5; -.
DR PRIDE; Q9UKN5; -.
DR ProteomicsDB; 84824; -.
DR ABCD; Q9UKN5; 1 sequenced antibody.
DR Antibodypedia; 18264; 292 antibodies from 32 providers.
DR DNASU; 11108; -.
DR Ensembl; ENST00000228437.10; ENSP00000228437.5; ENSG00000110851.12.
DR GeneID; 11108; -.
DR KEGG; hsa:11108; -.
DR MANE-Select; ENST00000228437.10; ENSP00000228437.5; NM_012406.4; NP_036538.3.
DR UCSC; uc001tmp.4; human.
DR CTD; 11108; -.
DR DisGeNET; 11108; -.
DR GeneCards; PRDM4; -.
DR HGNC; HGNC:9348; PRDM4.
DR HPA; ENSG00000110851; Low tissue specificity.
DR MIM; 605780; gene.
DR neXtProt; NX_Q9UKN5; -.
DR OpenTargets; ENSG00000110851; -.
DR PharmGKB; PA33716; -.
DR VEuPathDB; HostDB:ENSG00000110851; -.
DR eggNOG; KOG1721; Eukaryota.
DR eggNOG; KOG2461; Eukaryota.
DR GeneTree; ENSGT00940000156443; -.
DR HOGENOM; CLU_019772_0_0_1; -.
DR InParanoid; Q9UKN5; -.
DR OMA; RDYAQQM; -.
DR OrthoDB; 1318335at2759; -.
DR PhylomeDB; Q9UKN5; -.
DR TreeFam; TF332513; -.
DR PathwayCommons; Q9UKN5; -.
DR Reactome; R-HSA-193670; p75NTR negatively regulates cell cycle via SC1.
DR SignaLink; Q9UKN5; -.
DR BioGRID-ORCS; 11108; 13 hits in 1103 CRISPR screens.
DR ChiTaRS; PRDM4; human.
DR EvolutionaryTrace; Q9UKN5; -.
DR GenomeRNAi; 11108; -.
DR Pharos; Q9UKN5; Tbio.
DR PRO; PR:Q9UKN5; -.
DR Proteomes; UP000005640; Chromosome 12.
DR RNAct; Q9UKN5; protein.
DR Bgee; ENSG00000110851; Expressed in oocyte and 211 other tissues.
DR ExpressionAtlas; Q9UKN5; baseline and differential.
DR Genevisible; Q9UKN5; HS.
DR GO; GO:0005737; C:cytoplasm; IEA:Ensembl.
DR GO; GO:0035097; C:histone methyltransferase complex; NAS:ParkinsonsUK-UCL.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0001228; F:DNA-binding transcription activator activity, RNA polymerase II-specific; ISS:ARUK-UCL.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:1990226; F:histone methyltransferase binding; NAS:ParkinsonsUK-UCL.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; ISS:ARUK-UCL.
DR GO; GO:1990837; F:sequence-specific double-stranded DNA binding; IDA:ARUK-UCL.
DR GO; GO:0043985; P:histone H4-R3 methylation; NAS:ParkinsonsUK-UCL.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISS:ARUK-UCL.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IEA:InterPro.
DR CDD; cd19189; PR-SET_PRDM4; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR017124; PRDM4.
DR InterPro; IPR044404; PRDM4_PR/SET.
DR InterPro; IPR041493; PRDM4_Znf_knuckle.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF00096; zf-C2H2; 2.
DR Pfam; PF18445; zf_PR_Knuckle; 1.
DR PIRSF; PIRSF037161; PRDM4; 1.
DR SMART; SM00355; ZnF_C2H2; 7.
DR SUPFAM; SSF57667; SSF57667; 3.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 5.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 6.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Metal-binding; Methyltransferase; Nucleus;
KW Reference proteome; Repeat; S-adenosyl-L-methionine; Transcription;
KW Transcription regulation; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..801
FT /note="PR domain zinc finger protein 4"
FT /id="PRO_0000047760"
FT DOMAIN 412..529
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 545..566
FT /note="C2H2-type 1; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 618..640
FT /note="C2H2-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 646..668
FT /note="C2H2-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 674..696
FT /note="C2H2-type 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 702..724
FT /note="C2H2-type 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 730..752
FT /note="C2H2-type 6; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 751..782
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 761..778
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 16
FT /note="E -> A (in Ref. 1; AAD55249)"
FT /evidence="ECO:0000305"
FT CONFLICT 580
FT /note="H -> I (in Ref. 1; AAD55249)"
FT /evidence="ECO:0000305"
FT CONFLICT 608
FT /note="H -> Y (in Ref. 1; AAD55249)"
FT /evidence="ECO:0000305"
FT CONFLICT 662..663
FT /note="ES -> GV (in Ref. 1; AAD55249)"
FT /evidence="ECO:0000305"
FT STRAND 374..377
FT /evidence="ECO:0007829|PDB:2L9Z"
FT HELIX 378..380
FT /evidence="ECO:0007829|PDB:2L9Z"
FT STRAND 382..388
FT /evidence="ECO:0007829|PDB:2L9Z"
FT TURN 389..391
FT /evidence="ECO:0007829|PDB:2L9Z"
FT HELIX 405..408
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 414..418
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 425..431
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 445..447
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 462..468
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 471..477
FT /evidence="ECO:0007829|PDB:3DB5"
FT TURN 481..483
FT /evidence="ECO:0007829|PDB:3DB5"
FT HELIX 486..489
FT /evidence="ECO:0007829|PDB:3DB5"
FT TURN 496..498
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 501..506
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 509..516
FT /evidence="ECO:0007829|PDB:3DB5"
FT STRAND 525..528
FT /evidence="ECO:0007829|PDB:3DB5"
FT HELIX 531..536
FT /evidence="ECO:0007829|PDB:3DB5"
SQ SEQUENCE 801 AA; 87920 MW; 13B9B94F0825D113 CRC64;
MHHRMNEMNL SPVGMEQLTS SSVSNALPVS GSHLGLAASP THSAIPAPGL PVAIPNLGPS
LSSLPSALSL MLPMGIGDRG VMCGLPERNY TLPPPPYPHL ESSYFRTILP GILSYLADRP
PPQYIHPNSI NVDGNTALSI TNNPSALDPY QSNGNVGLEP GIVSIDSRSV NTHGAQSLHP
SDGHEVALDT AITMENVSRV TSPISTDGMA EELTMDGVAG EHSQIPNGSR SHEPLSVDSV
SNNLAADAVG HGGVIPMHGN GLELPVVMET DHIASRVNGM SDSALSDSIH TVAMSTNSVS
VALSTSHNLA SLESVSLHEV GLSLEPVAVS SITQEVAMGT GHVDVSSDSL SFVSPSLQME
DSNSNKENMA TLFTIWCTLC DRAYPSDCPE HGPVTFVPDT PIESRARLSL PKQLVLRQSI
VGAEVGVWTG ETIPVRTCFG PLIGQQSHSM EVAEWTDKAV NHIWKIYHNG VLEFCIITTD
ENECNWMMFV RKARNREEQN LVAYPHDGKI FFCTSQDIPP ENELLFYYSR DYAQQIGVPE
HPDVHLCNCG KECNSYTEFK AHLTSHIHNH LPTQGHSGSH GPSHSKERKW KCSMCPQAFI
SPSKLHVHFM GHMGMKPHKC DFCSKAFSDP SNLRTHLKIH TGQKNYRCTL CDKSFTQKAH
LESHMVIHTG EKNLKCDYCD KLFMRRQDLK QHVLIHTQER QIKCPKCDKL FLRTNHLKKH
LNSHEGKRDY VCEKCTKAYL TKYHLTRHLK TCKGPTSSSS APEEEEEDDS EEEDLADSVG
TEDCRINSAV YSADESLSAH K
