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Protein

Lysine-specific demethylase PHF2

Gene

Phf2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Enzyme 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

Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1338034. Phf2.

Subcellular locationi

  • Nucleusnucleolus By similarity
  • Chromosomecentromerekinetochore By similarity

GO - Cellular componenti

Complete GO annotation...

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
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, Phosphoprotein

Proteomic databases

EPDiQ9WTU0.
MaxQBiQ9WTU0.
PaxDbiQ9WTU0.
PeptideAtlasiQ9WTU0.
PRIDEiQ9WTU0.

PTM databases

iPTMnetiQ9WTU0.
PhosphoSitePlusiQ9WTU0.

Expressioni

Gene expression databases

BgeeiENSMUSG00000038025.
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. 4 interactors.
IntActiQ9WTU0. 1 interactor.
MINTiMINT-4107441.
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

Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

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.
OMAiEAHTKEA.
OrthoDBiEOG091G09DB.
PhylomeDBiQ9WTU0.
TreeFamiTF106480.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

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.

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. 4 interactors.
IntActiQ9WTU0. 1 interactor.
MINTiMINT-4107441.
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.
OMAiEAHTKEA.
OrthoDBiEOG091G09DB.
PhylomeDBiQ9WTU0.
TreeFamiTF106480.

Enzyme and pathway databases

ReactomeiR-MMU-3214842. HDMs demethylate histones.

Miscellaneous databases

PROiQ9WTU0.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000038025.
CleanExiMM_PHF2.
GenevisibleiQ9WTU0. MM.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHF2_MOUSE
AccessioniPrimary (citable) accession number: Q9WTU0
Secondary accession number(s): Q6A023, Q80WA8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 15, 2003
Last sequence update: August 15, 2003
Last modified: November 2, 2016
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.