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Protein

PR domain zinc finger protein 16

Gene

PRDM16

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

Functioni

Binds DNA and functions as a transcriptional regulator. Functions in the differentiation of brown adipose tissue (BAT) which is specialized in dissipating chemical energy in the form of heat in response to cold or excess feeding while white adipose tissue (WAT) is specialized in the storage of excess energy and the control of systemic metabolism. Together with CEBPB, regulates the differentiation of myoblastic precursors into brown adipose cells. Functions also as a repressor of TGF-beta signaling. Isoform 4 may regulate granulocytes differentiation.3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri230 – 253C2H2-type 1; atypicalPROSITE-ProRule annotationAdd BLAST24
Zinc fingeri281 – 303C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri309 – 331C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri337 – 360C2H2-type 4PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri366 – 388C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri394 – 416C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri423 – 445C2H2-type 7; atypicalPROSITE-ProRule annotationAdd BLAST23
Zinc fingeri951 – 973C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri979 – 1002C2H2-type 9PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri1008 – 1032C2H2-type 10PROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding, Repressor
Biological processDifferentiation, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3214841 PKMTs methylate histone lysines
SIGNORiQ9HAZ2

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 16Curated
Alternative name(s):
PR domain-containing protein 16Curated
Transcription factor MEL1Curated
Short name:
MDS1/EVI1-like gene 11 Publication
Gene namesi
Name:PRDM16Imported
Synonyms:KIAA1675Imported, MEL11 Publication, PFM13
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000142611.16
HGNCiHGNC:14000 PRDM16
MIMi605557 gene
neXtProtiNX_Q9HAZ2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Left ventricular non-compaction 8 (LVNC8)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of left ventricular non-compaction, a cardiomyopathy due to myocardial morphogenesis arrest and characterized by a hypertrophic left ventricle, a severely thickened 2-layered myocardium, numerous prominent trabeculations, deep intertrabecular recesses, and poor systolic function. Clinical manifestations are variable. Some affected individuals experience no symptoms at all, others develop heart failure. In some cases, left ventricular non-compaction is associated with other congenital heart anomalies. LVNC8 is an autosomal dominant condition.
See also OMIM:615373
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070214816N → S in LVNC8. 1 PublicationCorresponds to variant dbSNP:rs397514743EnsemblClinVar.1
Cardiomyopathy, dilated 1LL (CMD1LL)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death.
See also OMIM:615373
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070212271E → K in CMD1LL; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs200052869EnsemblClinVar.1
Natural variantiVAR_070213291P → L in CMD1LL; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs397514744EnsemblClinVar.1
Natural variantiVAR_070215887L → P in CMD1LL; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs202115331EnsemblClinVar.1
A chromosomal aberration involving PRDM16 is found in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Reciprocal translocation t(1;3)(p36;q21). Isoform 4 is specifically expressed in adult T-cell leukemia.2 Publications

Keywords - Diseasei

Cardiomyopathy, Disease mutation

Organism-specific databases

DisGeNETi63976
MalaCardsiPRDM16
MIMi615373 phenotype
OpenTargetsiENSG00000142611
Orphaneti1606 1p36 deletion syndrome
154 Familial isolated dilated cardiomyopathy
54260 Left ventricular noncompaction
PharmGKBiPA33714

Polymorphism and mutation databases

BioMutaiPRDM16
DMDMi259016328

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477731 – 1276PR domain zinc finger protein 16Add BLAST1276

Proteomic databases

MaxQBiQ9HAZ2
PaxDbiQ9HAZ2
PeptideAtlasiQ9HAZ2
PRIDEiQ9HAZ2
ProteomicsDBi81460
81461 [Q9HAZ2-2]
81462 [Q9HAZ2-3]
81463 [Q9HAZ2-4]

PTM databases

iPTMnetiQ9HAZ2
PhosphoSitePlusiQ9HAZ2

Expressioni

Tissue specificityi

Expressed in uterus and kidney. Expressed in both cardiomyocytes and interstitial cells.3 Publications

Gene expression databases

BgeeiENSG00000142611
CleanExiHS_PRDM16
ExpressionAtlasiQ9HAZ2 baseline and differential
GenevisibleiQ9HAZ2 HS

Organism-specific databases

HPAiHPA050343
HPA060467

Interactioni

Subunit structurei

Interacts with CEBPA, CEBPB and CEBPD; the interaction is direct. Interacts with PPARG and PPARA; controls brown adipocytes differentiation. Interacts with CTBP1 and CTBP2; represses the expression of WAT-specific genes. Interacts with PPARGC1A and PPARGC1B; interaction with PPARGC1A or PPARGC1B activates the transcription of BAT-specific gene (By similarity). Interacts with HDAC1, SKI, SMAD2 and SMAD3; the interaction with SKI promotes the recruitment of SMAD3-HDAC1 complex on the promoter of TGF-beta target genes (PubMed:19049980). Interacts with ZNF516; the interaction is direct and may play a role in the transcription of brown adipose tissue-specific gene (PubMed:25578880).By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Ctbp2P565462EBI-5282871,EBI-1384883From Mus musculus.

GO - Molecular functioni

  • activating transcription factor binding Source: UniProtKB
  • SMAD binding Source: Ensembl

Protein-protein interaction databases

BioGridi122023, 7 interactors
IntActiQ9HAZ2, 2 interactors
STRINGi9606.ENSP00000270722

Structurei

Secondary structure

11276
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi84 – 91Combined sources8
Turni92 – 94Combined sources3
Beta strandi95 – 102Combined sources8
Beta strandi126 – 129Combined sources4
Turni140 – 142Combined sources3
Turni153 – 155Combined sources3
Beta strandi161 – 163Combined sources3
Helixi167 – 170Combined sources4
Helixi178 – 180Combined sources3
Beta strandi183 – 188Combined sources6
Beta strandi191 – 198Combined sources8
Beta strandi212 – 215Combined sources4
Helixi216 – 219Combined sources4
Turni222 – 225Combined sources4

3D structure databases

ProteinModelPortaliQ9HAZ2
SMRiQ9HAZ2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini82 – 211SETPROSITE-ProRule annotationAdd BLAST130

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni679 – 1038Interaction with CTBP1, CTBP2 and ZNF516By similarityAdd BLAST360
Regioni739 – 1276Mediates interaction with SKI and regulation of TGF-beta signaling1 PublicationAdd BLAST538

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi459 – 557Pro-richAdd BLAST99

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri230 – 253C2H2-type 1; atypicalPROSITE-ProRule annotationAdd BLAST24
Zinc fingeri281 – 303C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri309 – 331C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri337 – 360C2H2-type 4PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri366 – 388C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri394 – 416C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri423 – 445C2H2-type 7; atypicalPROSITE-ProRule annotationAdd BLAST23
Zinc fingeri951 – 973C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri979 – 1002C2H2-type 9PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri1008 – 1032C2H2-type 10PROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721 Eukaryota
COG5048 LUCA
GeneTreeiENSGT00900000140928
HOVERGENiHBG005619
InParanoidiQ9HAZ2
KOiK22410
OMAiMSDGSDF
OrthoDBiEOG091G0BYE
PhylomeDBiQ9HAZ2
TreeFamiTF315309

Family and domain databases

InterProiView protein in InterPro
IPR030414 PRDM16
IPR001214 SET_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PANTHERiPTHR24393:SF5 PTHR24393:SF5, 1 hit
SMARTiView protein in SMART
SM00317 SET, 1 hit
SM00355 ZnF_C2H2, 10 hits
SUPFAMiSSF57667 SSF57667, 5 hits
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 8 hits
PS50157 ZINC_FINGER_C2H2_2, 10 hits

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative promoter usage and alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9HAZ2-1) [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

        10         20         30         40         50
MRSKARARKL AKSDGDVVNN MYEPNRDLLA SHSAEDEAED SAMSPIPVGP
60 70 80 90 100
PSPFPTSEDF TPKEGSPYEA PVYIPEDIPI PADFELRESS IPGAGLGVWA
110 120 130 140 150
KRKMEAGERL GPCVVVPRAA AKETDFGWEQ ILTDVEVSPQ EGCITKISED
160 170 180 190 200
LGSEKFCVDA NQAGAGSWLK YIRVACSCDD QNLTMCQISE QIYYKVIKDI
210 220 230 240 250
EPGEELLVHV KEGVYPLGTV PPGLDEEPTF RCDECDELFQ SKLDLRRHKK
260 270 280 290 300
YTCGSVGAAL YEGLAEELKP EGLGGGSGQA HECKDCERMF PNKYSLEQHM
310 320 330 340 350
VIHTEEREYK CDQCPKAFNW KSNLIRHQMS HDSGKRFECE NCVKVFTDPS
360 370 380 390 400
NLQRHIRSQH VGARAHACPD CGKTFATSSG LKQHKHIHST VKPFICEVCH
410 420 430 440 450
KSYTQFSNLC RHKRMHADCR TQIKCKDCGQ MFSTTSSLNK HRRFCEGKNH
460 470 480 490 500
YTPGGIFAPG LPLTPSPMMD KAKPSPSLNH ASLGFNEYFP SRPHPGSLPF
510 520 530 540 550
STAPPTFPAL TPGFPGIFPP SLYPRPPLLP PTSLLKSPLN HTQDAKLPSP
560 570 580 590 600
LGNPALPLVS AVSNSSQGTT AAAGPEEKFE SRLEDSCVEK LKTRSSDMSD
610 620 630 640 650
GSDFEDVNTT TGTDLDTTTG TGSDLDSDVD SDPDKDKGKG KSAEGQPKFG
660 670 680 690 700
GGLAPPGAPN SVAEVPVFYS QHSFFPPPDE QLLTATGAAG DSIKAIASIA
710 720 730 740 750
EKYFGPGFMG MQEKKLGSLP YHSAFPFQFL PNFPHSLYPF TDRALAHNLL
760 770 780 790 800
VKAEPKSPRD ALKVGGPSAE CPFDLTTKPK DVKPILPMPK GPSAPASGEE
810 820 830 840 850
QPLDLSIGSR ARASQNGGGR EPRKNHVYGE RKLGAGEGLP QVCPARMPQQ
860 870 880 890 900
PPLHYAKPSP FFMDPIYSRV EKRKVTDPVG ALKEKYLRPS PLLFHPQMSA
910 920 930 940 950
IETMTEKLES FAAMKADSGS SLQPLPHHPF NFRSPPPTLS DPILRKGKER
960 970 980 990 1000
YTCRYCGKIF PRSANLTRHL RTHTGEQPYR CKYCDRSFSI SSNLQRHVRN
1010 1020 1030 1040 1050
IHNKEKPFKC HLCNRCFGQQ TNLDRHLKKH EHENAPVSQH PGVLTNHLGT
1060 1070 1080 1090 1100
SASSPTSESD NHALLDEKED SYFSEIRNFI ANSEMNQAST RTEKRADMQI
1110 1120 1130 1140 1150
VDGSAQCPGL ASEKQEDVEE EDDDDLEEDD EDSLAGKSQD DTVSPAPEPQ
1160 1170 1180 1190 1200
AAYEDEEDEE PAASLAVGFD HTRRCAEDHE GGLLALEPMP TFGKGLDLRR
1210 1220 1230 1240 1250
AAEEAFEVKD VLNSTLDSEA LKHTLCRQAK NQAYAMMLSL SEDTPLHTPS
1260 1270
QGSLDAWLKV TGATSESGAF HPINHL
Length:1,276
Mass (Da):140,251
Last modified:September 22, 2009 - v3
Checksum:iAD16C5C0EE89A528
GO
Isoform 2 (identifier: Q9HAZ2-2) [UniParc]FASTAAdd to basket
Also known as: MEL1L

The sequence of this isoform differs from the canonical sequence as follows:
     1233-1251: Missing.

Note: No experimental confirmation available.
Show »
Length:1,257
Mass (Da):138,177
Checksum:i1CB045F5BBFE9D20
GO
Isoform 3 (identifier: Q9HAZ2-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     191-191: Q → QV
     868-868: Missing.

Note: No experimental confirmation available.
Show »
Length:1,276
Mass (Da):140,263
Checksum:iA5A073C5C5F26306
GO
Isoform 4 (identifier: Q9HAZ2-4) [UniParc]FASTAAdd to basket
Also known as: MEL1S

The sequence of this isoform differs from the canonical sequence as follows:
     1-184: Missing.

Note: Produced by alternative promoter usage.
Show »
Length:1,092
Mass (Da):120,338
Checksum:i7A24088D0A73B54F
GO

Sequence cautioni

The sequence BAB21766 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti50 – 52PPS → SPP in AAG33382 (Ref. 2) Curated3
Sequence conflicti324L → F in AAG33382 (Ref. 2) Curated1
Sequence conflicti491S → Y in AAG33382 (Ref. 2) Curated1
Sequence conflicti1022N → K in BAB84297 (PubMed:11050005).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070212271E → K in CMD1LL; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs200052869EnsemblClinVar.1
Natural variantiVAR_070213291P → L in CMD1LL; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs397514744EnsemblClinVar.1
Natural variantiVAR_031433533S → P3 PublicationsCorresponds to variant dbSNP:rs870124EnsemblClinVar.1
Natural variantiVAR_031434633P → L. Corresponds to variant dbSNP:rs2493292EnsemblClinVar.1
Natural variantiVAR_070214816N → S in LVNC8. 1 PublicationCorresponds to variant dbSNP:rs397514743EnsemblClinVar.1
Natural variantiVAR_070215887L → P in CMD1LL; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs202115331EnsemblClinVar.1
Natural variantiVAR_0702161101V → M1 PublicationCorresponds to variant dbSNP:rs201654872EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0380631 – 184Missing in isoform 4. CuratedAdd BLAST184
Alternative sequenceiVSP_038064191Q → QV in isoform 3. 1 Publication1
Alternative sequenceiVSP_038065868Missing in isoform 3. 1 Publication1
Alternative sequenceiVSP_0069321233 – 1251Missing in isoform 2. 1 PublicationAdd BLAST19

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB078876 mRNA Translation: BAB84297.1
AF294278 mRNA Translation: AAG33382.1
AB051462 mRNA Translation: BAB21766.2 Different initiation.
AL008733 Genomic DNA No translation available.
AL354743 Genomic DNA No translation available.
AL512383 Genomic DNA No translation available.
AL590438 Genomic DNA No translation available.
BC161614 mRNA Translation: AAI61614.1
CCDSiCCDS41236.2 [Q9HAZ2-1]
CCDS44048.2 [Q9HAZ2-2]
RefSeqiNP_071397.3, NM_022114.3 [Q9HAZ2-1]
NP_955533.2, NM_199454.2 [Q9HAZ2-2]
XP_011540247.1, XM_011541945.2 [Q9HAZ2-4]
UniGeneiHs.99500

Genome annotation databases

EnsembliENST00000270722; ENSP00000270722; ENSG00000142611 [Q9HAZ2-1]
ENST00000378391; ENSP00000367643; ENSG00000142611 [Q9HAZ2-2]
GeneIDi63976
KEGGihsa:63976
UCSCiuc001ake.4 human [Q9HAZ2-1]

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing, Chromosomal rearrangement, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPRD16_HUMAN
AccessioniPrimary (citable) accession number: Q9HAZ2
Secondary accession number(s): A6NHQ8
, B1AJP7, B1AJP8, B1AJP9, B1WB48, Q8WYJ9, Q9C0I8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: September 22, 2009
Last modified: July 18, 2018
This is version 171 of the entry and version 3 of the sequence. See 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 1
    Human chromosome 1: 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

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