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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei193 – 1931Alpha-ketoglutarateBy similarity
Binding sitei246 – 2461Alpha-ketoglutarateBy similarity
Metal bindingi249 – 2491Iron; catalyticPROSITE-ProRule annotation
Metal bindingi251 – 2511Iron; catalyticPROSITE-ProRule annotation
Binding sitei259 – 2591Alpha-ketoglutarateBy similarity
Binding sitei266 – 2661Alpha-ketoglutarateBy similarity
Metal bindingi321 – 3211Iron; catalyticPROSITE-ProRule annotation
Binding sitei323 – 3231Alpha-ketoglutarateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri5 – 5652PHD-typePROSITE-ProRule annotationAdd
BLAST

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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Kinetochore, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10961096Lysine-specific demethylase PHF2PRO_0000059291Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei474 – 4741PhosphoserineCombined sources
Modified residuei479 – 4791PhosphothreonineBy similarity
Modified residuei536 – 5361PhosphoserineBy similarity
Modified residuei651 – 6511PhosphoserineCombined sources
Modified residuei677 – 6771PhosphoserineCombined sources
Modified residuei701 – 7011PhosphoserineBy similarity
Modified residuei716 – 7161N6-acetyllysineCombined sources
Modified residuei724 – 7241PhosphotyrosineCombined sources
Modified residuei726 – 7261PhosphoserineCombined sources
Modified residuei729 – 7291PhosphoserineCombined sources
Modified residuei730 – 7301PhosphoserineCombined sources
Modified residuei734 – 7341PhosphoserineCombined sources
Modified residuei873 – 8731PhosphoserineCombined sources
Modified residuei876 – 8761PhosphoserineCombined sources
Modified residuei893 – 8931PhosphoserineCombined sources
Modified residuei1057 – 10571Phosphoserine; by PKABy similarity

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.
PRIDEiQ9WTU0.

PTM databases

iPTMnetiQ9WTU0.
PhosphoSiteiQ9WTU0.

Expressioni

Gene expression databases

BgeeiQ9WTU0.
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 interactions.
IntActiQ9WTU0. 1 interaction.
MINTiMINT-4107441.
STRINGi10090.ENSMUSP00000047308.

Structurei

3D structure databases

ProteinModelPortaliQ9WTU0.
SMRiQ9WTU0. Positions 1-444.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini197 – 353157JmjCPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi487 – 606120Lys-richAdd
BLAST
Compositional biasi959 – 102163Ser-richAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri5 – 5652PHD-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1633. Eukaryota.
ENOG410Y2FD. LUCA.
GeneTreeiENSGT00550000074396.
HOGENOMiHOG000231232.
HOVERGENiHBG045631.
InParanoidiQ9WTU0.
KOiK19414.
OMAiEAHTKEA.
OrthoDBiEOG73JKV9.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti938 – 9381Q → L in AAD21792 (PubMed:10051327).Curated
Sequence conflicti955 – 9551P → S in BAD32273 (PubMed:15368895).Curated

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. Positions 1-444.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202144. 4 interactions.
IntActiQ9WTU0. 1 interaction.
MINTiMINT-4107441.
STRINGi10090.ENSMUSP00000047308.

PTM databases

iPTMnetiQ9WTU0.
PhosphoSiteiQ9WTU0.

Proteomic databases

EPDiQ9WTU0.
MaxQBiQ9WTU0.
PaxDbiQ9WTU0.
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.
OrthoDBiEOG73JKV9.
PhylomeDBiQ9WTU0.
TreeFamiTF106480.

Enzyme and pathway databases

ReactomeiR-MMU-3214842. HDMs demethylate histones.

Miscellaneous databases

PROiQ9WTU0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9WTU0.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "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: Limb.
  4. "Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
    Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H., Nagase T., Ohara O., Koga H.
    DNA Res. 11:205-218(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 59-1096.
  5. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-474; SER-651; SER-677; TYR-724; SER-726; SER-729; SER-730; SER-734; SER-873; SER-876 AND SER-893, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.
  6. "Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation."
    Wen H., Li J., Song T., Lu M., Kan P.Y., Lee M.G., Sha B., Shi X.
    J. Biol. Chem. 285:9322-9326(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY.
  7. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-716, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

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: June 8, 2016
This is version 114 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.