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Protein

Lysine-specific demethylase PHF2

Gene

Phf2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA (By similarity).By similarity

Caution

In contrast to the related histone demethylases JHDM1D and PHF8, the conserved active His in position 321 is replaced by a Tyr. However, the presence of a Tyr residue neither affects binding to the catalytic iron nor abolishes demethylase activity.Curated

Activity regulationi

Enzymatically inactive by itself, and become active following phosphorylation by PKA.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei193Alpha-ketoglutarateBy similarity1
Binding sitei246Alpha-ketoglutarateBy similarity1
Metal bindingi249Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi251Iron; catalyticPROSITE-ProRule annotation1
Binding sitei259Alpha-ketoglutarateBy similarity1
Binding sitei266Alpha-ketoglutarateBy similarity1
Metal bindingi321Iron; catalyticPROSITE-ProRule annotation1
Binding sitei323Alpha-ketoglutarateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri5 – 56PHD-typePROSITE-ProRule annotationAdd BLAST52

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, Chromatin regulator, Dioxygenase, Oxidoreductase
Biological processTranscription, Transcription regulation
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-3214842 HDMs demethylate histones

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase PHF2 (EC:1.14.11.-)
Alternative name(s):
GRC5
PHD finger protein 2
Gene namesi
Name:Phf2
Synonyms:Kiaa0662
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1338034 Phf2

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

Centromere, Chromosome, Kinetochore, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000592911 – 1096Lysine-specific demethylase PHF2Add BLAST1096

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei474PhosphoserineCombined sources1
Modified residuei479PhosphothreonineBy similarity1
Modified residuei536PhosphoserineBy similarity1
Modified residuei651PhosphoserineCombined sources1
Modified residuei677PhosphoserineCombined sources1
Modified residuei701PhosphoserineBy similarity1
Cross-linki707Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei716N6-acetyllysineCombined sources1
Modified residuei724PhosphotyrosineCombined sources1
Modified residuei726PhosphoserineCombined sources1
Modified residuei729PhosphoserineCombined sources1
Modified residuei730PhosphoserineCombined sources1
Modified residuei734PhosphoserineCombined sources1
Modified residuei873PhosphoserineCombined sources1
Modified residuei876PhosphoserineCombined sources1
Modified residuei893PhosphoserineCombined sources1
Modified residuei1057Phosphoserine; by PKABy similarity1

Post-translational modificationi

Phosphorylated by PKA on specific serine residues, leading to the formation of an active lysine demethylase complex.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9WTU0
MaxQBiQ9WTU0
PaxDbiQ9WTU0
PeptideAtlasiQ9WTU0
PRIDEiQ9WTU0

PTM databases

iPTMnetiQ9WTU0
PhosphoSitePlusiQ9WTU0

Expressioni

Gene expression databases

BgeeiENSMUSG00000038025 Expressed in 293 organ(s), highest expression level in ascending aorta
CleanExiMM_PHF2
GenevisibleiQ9WTU0 MM

Interactioni

Subunit structurei

Component of the PHF2-ARID5B complex, at least composed of PHF2 and ARID5B. Interacts with HNF4A and NR1H4 (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi202144, 5 interactors
IntActiQ9WTU0, 1 interactor
MINTiQ9WTU0
STRINGi10090.ENSMUSP00000047308

Structurei

3D structure databases

ProteinModelPortaliQ9WTU0
SMRiQ9WTU0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini197 – 353JmjCPROSITE-ProRule annotationAdd BLAST157

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi487 – 606Lys-richAdd BLAST120
Compositional biasi959 – 1021Ser-richAdd BLAST63

Domaini

The PHD-type zinc finger mediates the binding to H3K4me2 and H3K4me3.By similarity

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri5 – 56PHD-typePROSITE-ProRule annotationAdd BLAST52

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1633 Eukaryota
ENOG410Y2FD LUCA
GeneTreeiENSGT00550000074396
HOGENOMiHOG000231232
HOVERGENiHBG045631
InParanoidiQ9WTU0
KOiK19414
OMAiDSCLQTT
OrthoDBiEOG091G09DB
PhylomeDBiQ9WTU0
TreeFamiTF106480

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS01359 ZF_PHD_1, 1 hit
PS50016 ZF_PHD_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q9WTU0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MATVPVYCVC RLPYDVTRFM IECDACKDWF HGSCVGVEEE EAPDIDIYHC
60 70 80 90 100
PNCEKTHGKS TLKKKRTWHK HGPGPTPDVK PVQNGSQLFI KELRSRTFPS
110 120 130 140 150
AEDVVSRVPG SQLTVGYMEE HGFTEPILVP KKDGLGLAVP APTFYVSDVE
160 170 180 190 200
NYVGPERSVD VTDVTKQKDC KMKLKEFVDY YYSTNRKRVL NVTNLEFSDT
210 220 230 240 250
RMSSFVEPPD IVKKLSWVEN YWPDDALLAK PKVTKYCLIC VKDSYTDFHI
260 270 280 290 300
DSGGASAWYH VLKGEKIFYL IRPASANISL YERWRSASNH SEMFFADQVD
310 320 330 340 350
RCYKCTVKQG QTLFIPSGWI YATLTPVDCL AFAGHFLHSL SVEMQMRAYE
360 370 380 390 400
VERRLKLGSL TQFPNFETAC WYMGKHLLEA FKGSHKSGKQ LPPHLVQGAK
410 420 430 440 450
ILNGAFRSWT KKQALAEHED ELPEHFRPSQ LIKDLAKEIR LSENASKTVR
460 470 480 490 500
PEVNAAASSD EVCDGDREKE EPPSPVETTP PRSLLEKVSK KKTSKTVKMP
510 520 530 540 550
KPSKIPKPPK SPKPPKTLKL KDGSKKKGKK CKESASPTIP NLDLLEAHTK
560 570 580 590 600
EALTKMEPPK KGKTPKSVLS VPNKDTVHTQ NDMERLEIRE QTKSKSEAKW
610 620 630 640 650
KYKNSKPDSL LKMEEEQRLE KSPLAGNKDK FSFSFSNRKL LGSKALRPPS
660 670 680 690 700
SPGVFGALQS FKEDKAKPVR DEYEYVSDDG ELKIDEFPIR RKKSAPKRDL
710 720 730 740 750
SFLLDKKEAL LMPTSKPKLD SAVYKSDDSS DEGSLHIDTD TKPGRNAKVK
760 770 780 790 800
KESGSSAAGI LDLLQASEEV GALEYNPNSQ PPASPSTQEA IQGMLSMANL
810 820 830 840 850
QASDSCLQTT WGTGQAKGGS LAAHGARKIG GGNKGTGKRL LKRTAKNSVD
860 870 880 890 900
LEDYEEQDHL DACFKDSDYV YPSLESDEDN PVFKSRSKKR KGSDDAPYSP
910 920 930 940 950
TARVGPSVPR QDRPVREGTR VASIETGLAA AAAKLSQQEE QKNRKKKNTK
960 970 980 990 1000
RKPAPNTASP SISTSASAST GTTSASTTPA STTPASTTPA STTPASTSTA
1010 1020 1030 1040 1050
SSQASQEGSS PEPPPESHSS SLADHEYTAA GTFSGSQAGR ASQPMAPGVF
1060 1070 1080 1090
LTQRRPSASS PNNTAAKGKR TKKGMATAKQ RLGKILKIHR NGKLLL
Length:1,096
Mass (Da):120,814
Last modified:August 15, 2003 - v2
Checksum:i778B822C007D8860
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti938Q → L in AAD21792 (PubMed:10051327).Curated1
Sequence conflicti955P → S in BAD32273 (PubMed:15368895).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF043726 mRNA Translation: AAD21792.1
AC109249 Genomic DNA No translation available.
BC051633 mRNA Translation: AAH51633.1
AK172995 mRNA Translation: BAD32273.1
CCDSiCCDS26496.1
RefSeqiNP_035208.2, NM_011078.3
UniGeneiMm.486213

Genome annotation databases

EnsembliENSMUST00000035540; ENSMUSP00000047308; ENSMUSG00000038025
GeneIDi18676
KEGGimmu:18676
UCSCiuc007qim.1 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF043726 mRNA Translation: AAD21792.1
AC109249 Genomic DNA No translation available.
BC051633 mRNA Translation: AAH51633.1
AK172995 mRNA Translation: BAD32273.1
CCDSiCCDS26496.1
RefSeqiNP_035208.2, NM_011078.3
UniGeneiMm.486213

3D structure databases

ProteinModelPortaliQ9WTU0
SMRiQ9WTU0
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202144, 5 interactors
IntActiQ9WTU0, 1 interactor
MINTiQ9WTU0
STRINGi10090.ENSMUSP00000047308

PTM databases

iPTMnetiQ9WTU0
PhosphoSitePlusiQ9WTU0

Proteomic databases

EPDiQ9WTU0
MaxQBiQ9WTU0
PaxDbiQ9WTU0
PeptideAtlasiQ9WTU0
PRIDEiQ9WTU0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000035540; ENSMUSP00000047308; ENSMUSG00000038025
GeneIDi18676
KEGGimmu:18676
UCSCiuc007qim.1 mouse

Organism-specific databases

CTDi5253
MGIiMGI:1338034 Phf2
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1633 Eukaryota
ENOG410Y2FD LUCA
GeneTreeiENSGT00550000074396
HOGENOMiHOG000231232
HOVERGENiHBG045631
InParanoidiQ9WTU0
KOiK19414
OMAiDSCLQTT
OrthoDBiEOG091G09DB
PhylomeDBiQ9WTU0
TreeFamiTF106480

Enzyme and pathway databases

ReactomeiR-MMU-3214842 HDMs demethylate histones

Miscellaneous databases

PROiPR:Q9WTU0
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000038025 Expressed in 293 organ(s), highest expression level in ascending aorta
CleanExiMM_PHF2
GenevisibleiQ9WTU0 MM

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS01359 ZF_PHD_1, 1 hit
PS50016 ZF_PHD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPHF2_MOUSE
AccessioniPrimary (citable) accession number: Q9WTU0
Secondary accession number(s): Q6A023, Q80WA8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 15, 2003
Last sequence update: August 15, 2003
Last modified: November 7, 2018
This is version 125 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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Main funding by: National Institutes of Health

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