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Protein

PR domain zinc finger protein 4

Gene

PRDM4

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

Functioni

May function as a transcription factor involved in cell differentiation.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri545 – 56622C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri618 – 64023C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri646 – 66823C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri674 – 69623C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri702 – 72423C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri730 – 75223C2H2-type 6; atypicalPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • methyltransferase activity Source: UniProtKB-KW
  • zinc ion binding Source: ProtInc

GO - Biological processi

  • cell proliferation Source: ProtInc
  • cellular response to nutrient Source: Ensembl
  • negative regulation of cell cycle Source: Reactome
  • negative regulation of cell growth Source: Ensembl
  • neurotrophin TRK receptor signaling pathway Source: Reactome
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • signal transduction Source: ProtInc
  • transcription from RNA polymerase II promoter Source: ProtInc
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiREACT_13695. p75NTR negatively regulates cell cycle via SC1.

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 4 (EC:2.1.1.-)
Alternative name(s):
PR domain-containing protein 4
Gene namesi
Name:PRDM4
Synonyms:PFM1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:9348. PRDM4.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33716.

Polymorphism and mutation databases

BioMutaiPRDM4.
DMDMi25008960.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 801801PR domain zinc finger protein 4PRO_0000047760Add
BLAST

Proteomic databases

MaxQBiQ9UKN5.
PaxDbiQ9UKN5.
PRIDEiQ9UKN5.

PTM databases

PhosphoSiteiQ9UKN5.

Expressioni

Tissue specificityi

Expressed in many tissues. Highly expressed in ovary, testis, pancreas, brain, heart and prostate.

Gene expression databases

BgeeiQ9UKN5.
CleanExiHS_PRDM4.
ExpressionAtlasiQ9UKN5. baseline and differential.
GenevisibleiQ9UKN5. HS.

Organism-specific databases

HPAiHPA024322.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
CTNNBL1Q8WYA63EBI-2803427,EBI-748128
MSRB3Q8IXL73EBI-2803427,EBI-8634060

Protein-protein interaction databases

BioGridi116288. 10 interactions.
IntActiQ9UKN5. 5 interactions.
MINTiMINT-1183894.
STRINGi9606.ENSP00000228437.

Structurei

Secondary structure

1
801
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi374 – 3774Combined sources
Helixi378 – 3803Combined sources
Beta strandi382 – 3887Combined sources
Turni389 – 3913Combined sources
Helixi405 – 4084Combined sources
Beta strandi414 – 4185Combined sources
Beta strandi425 – 4317Combined sources
Beta strandi445 – 4473Combined sources
Beta strandi462 – 4687Combined sources
Beta strandi471 – 4777Combined sources
Turni481 – 4833Combined sources
Helixi486 – 4894Combined sources
Turni496 – 4983Combined sources
Beta strandi501 – 5066Combined sources
Beta strandi509 – 5168Combined sources
Beta strandi525 – 5284Combined sources
Helixi531 – 5366Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L9ZNMR-A366-402[»]
3DB5X-ray2.15A/B390-540[»]
ProteinModelPortaliQ9UKN5.
SMRiQ9UKN5. Positions 365-751.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UKN5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini412 – 529118SETPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 6 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri545 – 56622C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri618 – 64023C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri646 – 66823C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri674 – 69623C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri702 – 72423C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri730 – 75223C2H2-type 6; atypicalPROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5048.
GeneTreeiENSGT00770000120502.
HOGENOMiHOG000060213.
HOVERGENiHBG053672.
InParanoidiQ9UKN5.
KOiK12463.
OMAiIPVRTCF.
OrthoDBiEOG7R830T.
PhylomeDBiQ9UKN5.
TreeFamiTF332513.

Family and domain databases

Gene3Di3.30.160.60. 6 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR017124. Znf_PRDM4.
[Graphical view]
PfamiPF00096. zf-C2H2. 1 hit.
[Graphical view]
PIRSFiPIRSF037161. PRDM4. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 7 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 5 hits.
PS50157. ZINC_FINGER_C2H2_2. 6 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9UKN5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHHRMNEMNL SPVGMEQLTS SSVSNALPVS GSHLGLAASP THSAIPAPGL
60 70 80 90 100
PVAIPNLGPS LSSLPSALSL MLPMGIGDRG VMCGLPERNY TLPPPPYPHL
110 120 130 140 150
ESSYFRTILP GILSYLADRP PPQYIHPNSI NVDGNTALSI TNNPSALDPY
160 170 180 190 200
QSNGNVGLEP GIVSIDSRSV NTHGAQSLHP SDGHEVALDT AITMENVSRV
210 220 230 240 250
TSPISTDGMA EELTMDGVAG EHSQIPNGSR SHEPLSVDSV SNNLAADAVG
260 270 280 290 300
HGGVIPMHGN GLELPVVMET DHIASRVNGM SDSALSDSIH TVAMSTNSVS
310 320 330 340 350
VALSTSHNLA SLESVSLHEV GLSLEPVAVS SITQEVAMGT GHVDVSSDSL
360 370 380 390 400
SFVSPSLQME DSNSNKENMA TLFTIWCTLC DRAYPSDCPE HGPVTFVPDT
410 420 430 440 450
PIESRARLSL PKQLVLRQSI VGAEVGVWTG ETIPVRTCFG PLIGQQSHSM
460 470 480 490 500
EVAEWTDKAV NHIWKIYHNG VLEFCIITTD ENECNWMMFV RKARNREEQN
510 520 530 540 550
LVAYPHDGKI FFCTSQDIPP ENELLFYYSR DYAQQIGVPE HPDVHLCNCG
560 570 580 590 600
KECNSYTEFK AHLTSHIHNH LPTQGHSGSH GPSHSKERKW KCSMCPQAFI
610 620 630 640 650
SPSKLHVHFM GHMGMKPHKC DFCSKAFSDP SNLRTHLKIH TGQKNYRCTL
660 670 680 690 700
CDKSFTQKAH LESHMVIHTG EKNLKCDYCD KLFMRRQDLK QHVLIHTQER
710 720 730 740 750
QIKCPKCDKL FLRTNHLKKH LNSHEGKRDY VCEKCTKAYL TKYHLTRHLK
760 770 780 790 800
TCKGPTSSSS APEEEEEDDS EEEDLADSVG TEDCRINSAV YSADESLSAH

K
Length:801
Mass (Da):87,920
Last modified:November 8, 2002 - v3
Checksum:i13B9B94F0825D113
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti16 – 161E → A in AAD55249 (PubMed:10552934).Curated
Sequence conflicti580 – 5801H → I in AAD55249 (PubMed:10552934).Curated
Sequence conflicti608 – 6081H → Y in AAD55249 (PubMed:10552934).Curated
Sequence conflicti662 – 6632ES → GV in AAD55249 (PubMed:10552934).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF144757 mRNA. Translation: AAD55249.2.
BC035581 mRNA. Translation: AAH35581.1.
AL133083 mRNA. Translation: CAB61401.1.
CCDSiCCDS9115.1.
PIRiT42688.
RefSeqiNP_036538.3. NM_012406.3.
UniGeneiHs.506655.

Genome annotation databases

EnsembliENST00000228437; ENSP00000228437; ENSG00000110851.
GeneIDi11108.
KEGGihsa:11108.
UCSCiuc001tmp.3. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF144757 mRNA. Translation: AAD55249.2.
BC035581 mRNA. Translation: AAH35581.1.
AL133083 mRNA. Translation: CAB61401.1.
CCDSiCCDS9115.1.
PIRiT42688.
RefSeqiNP_036538.3. NM_012406.3.
UniGeneiHs.506655.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L9ZNMR-A366-402[»]
3DB5X-ray2.15A/B390-540[»]
ProteinModelPortaliQ9UKN5.
SMRiQ9UKN5. Positions 365-751.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116288. 10 interactions.
IntActiQ9UKN5. 5 interactions.
MINTiMINT-1183894.
STRINGi9606.ENSP00000228437.

PTM databases

PhosphoSiteiQ9UKN5.

Polymorphism and mutation databases

BioMutaiPRDM4.
DMDMi25008960.

Proteomic databases

MaxQBiQ9UKN5.
PaxDbiQ9UKN5.
PRIDEiQ9UKN5.

Protocols and materials databases

DNASUi11108.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000228437; ENSP00000228437; ENSG00000110851.
GeneIDi11108.
KEGGihsa:11108.
UCSCiuc001tmp.3. human.

Organism-specific databases

CTDi11108.
GeneCardsiGC12M108126.
HGNCiHGNC:9348. PRDM4.
HPAiHPA024322.
MIMi605780. gene.
neXtProtiNX_Q9UKN5.
PharmGKBiPA33716.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5048.
GeneTreeiENSGT00770000120502.
HOGENOMiHOG000060213.
HOVERGENiHBG053672.
InParanoidiQ9UKN5.
KOiK12463.
OMAiIPVRTCF.
OrthoDBiEOG7R830T.
PhylomeDBiQ9UKN5.
TreeFamiTF332513.

Enzyme and pathway databases

ReactomeiREACT_13695. p75NTR negatively regulates cell cycle via SC1.

Miscellaneous databases

EvolutionaryTraceiQ9UKN5.
GenomeRNAii11108.
NextBioi42234.
PROiQ9UKN5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9UKN5.
CleanExiHS_PRDM4.
ExpressionAtlasiQ9UKN5. baseline and differential.
GenevisibleiQ9UKN5. HS.

Family and domain databases

Gene3Di3.30.160.60. 6 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR017124. Znf_PRDM4.
[Graphical view]
PfamiPF00096. zf-C2H2. 1 hit.
[Graphical view]
PIRSFiPIRSF037161. PRDM4. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 7 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 5 hits.
PS50157. ZINC_FINGER_C2H2_2. 6 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "PFM1 (PRDM4), a new member of the PR-domain family, maps to a tumor suppressor locus on human chromosome 12q23-q24.1."
    Yang X.-H., Huang S.
    Genomics 61:319-325(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "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].
    Tissue: Testis.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 77-801.
    Tissue: Testis.
  4. "The crystal structure of methyltransferase domain of human PR domain-containing protein 4."
    Structural genomics consortium (SGC)
    Submitted (AUG-2008) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 390-540.

Entry informationi

Entry nameiPRDM4_HUMAN
AccessioniPrimary (citable) accession number: Q9UKN5
Secondary accession number(s): Q9UFA6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: November 8, 2002
Last modified: July 22, 2015
This is version 138 of the entry and version 3 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 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.