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Q80TJ7 (PHF8_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone lysine demethylase PHF8

EC=1.14.11.27
Alternative name(s):
PHD finger protein 8
Gene names
Name:Phf8
Synonyms:Kiaa1111
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1023 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3 By similarity.

Catalytic activity

Protein N6,N(6)-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO2.

Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2.

Cofactor

Binds 1 Fe2+ ion per subunit By similarity.

Subunit structure

Interacts with POLR1B, UBTF, SETD1A, HCFC1, E2F1 and ZNF711 By similarity.

Subcellular location

Nucleus By similarity. Nucleusnucleolus By similarity. Note: Recruited to H3K4me3 sites on chromatin during interphase. Dissociates from chromatin when cells enter mitosis By similarity.

Domain

The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 promotes its access to H3K9me2 By similarity.

The linker region is a critical determinant of demethylase specificity. It enables the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3 By similarity.

Post-translational modification

Phosphorylation at Ser-33 and Ser-84 are required for dissociation from chromatin and accumulation of H4K20Me1 levels during prophase By similarity.

Sequence similarities

Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.

Contains 1 JmjC domain.

Contains 1 PHD-type zinc finger.

Sequence caution

The sequence CAM17163.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
   Biological processCell cycle
Transcription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainZinc-finger
   LigandIron
Metal-binding
Zinc
   Molecular functionActivator
Chromatin regulator
Dioxygenase
Oxidoreductase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processG1/S transition of mitotic cell cycle

Inferred from sequence or structural similarity. Source: UniProtKB

brain development

Inferred from sequence or structural similarity. Source: UniProtKB

histone H3-K27 demethylation

Inferred from sequence or structural similarity. Source: UniProtKB

histone H3-K36 demethylation

Inferred from sequence or structural similarity. Source: UniProtKB

histone H3-K9 demethylation

Inferred from sequence or structural similarity. Source: UniProtKB

histone H4-K20 demethylation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of chromatin silencing at rDNA

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription from RNA polymerase I promoter

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from sequence or structural similarity. Source: UniProtKB

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleolus

Inferred from sequence or structural similarity. Source: UniProtKB

nucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionchromatin binding

Inferred from sequence or structural similarity. Source: UniProtKB

histone demethylase activity

Inferred from sequence or structural similarity. Source: UniProtKB

histone demethylase activity (H3-K27 specific)

Inferred from sequence or structural similarity. Source: UniProtKB

histone demethylase activity (H3-K36 specific)

Inferred from sequence or structural similarity. Source: UniProtKB

histone demethylase activity (H3-K9 specific)

Inferred from sequence or structural similarity. Source: UniProtKB

histone demethylase activity (H4-K20 specific)

Inferred from sequence or structural similarity. Source: UniProtKB

iron ion binding

Inferred from sequence or structural similarity. Source: UniProtKB

methylated histone binding

Inferred from sequence or structural similarity. Source: UniProtKB

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors

Inferred from sequence or structural similarity. Source: UniProtKB

zinc ion binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q80TJ7-1)

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.
Isoform 2 (identifier: Q80TJ7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     442-542: Missing.
     883-896: ELQKAQKKKYIKKK → VRVDTQLVALLLMT
     897-1023: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q80TJ7-3)

The sequence of this isoform differs from the canonical sequence as follows:
     442-464: DIFQQNVGKTSNIFGLQRIFPAG → VRSMGEGKAFGKGWRLKWQVRTL
     465-1023: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10231023Histone lysine demethylase PHF8
PRO_0000059296

Regions

Domain195 – 351157JmjC
Zinc finger5 – 5652PHD-type
Region65 – 7915Linker By similarity
Compositional bias733 – 77139Ser-rich

Sites

Metal binding2471Iron; catalytic By similarity
Metal binding2491Iron; catalytic By similarity
Metal binding3191Iron; catalytic By similarity
Binding site2441Substrate By similarity
Binding site2641Substrate By similarity

Amino acid modifications

Modified residue331Phosphoserine; by CDK1 By similarity
Modified residue841Phosphoserine; by CDK1 By similarity
Modified residue6151Phosphoserine Ref.6
Modified residue6691Phosphothreonine By similarity
Modified residue6701Phosphothreonine By similarity
Modified residue7681Phosphoserine By similarity
Modified residue8171Phosphoserine By similarity
Modified residue8201Phosphoserine Ref.5 Ref.6
Modified residue8431Phosphoserine By similarity

Natural variations

Alternative sequence442 – 542101Missing in isoform 2.
VSP_014966
Alternative sequence442 – 46423DIFQQ…IFPAG → VRSMGEGKAFGKGWRLKWQV RTL in isoform 3.
VSP_014967
Alternative sequence465 – 1023559Missing in isoform 3.
VSP_014968
Alternative sequence883 – 89614ELQKA…YIKKK → VRVDTQLVALLLMT in isoform 2.
VSP_014969
Alternative sequence897 – 1023127Missing in isoform 2.
VSP_014970

Secondary structure

............... 1023
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified August 16, 2005. Version 2.
Checksum: 7B9351944C000487

FASTA1,023113,553
        10         20         30         40         50         60 
MASVPVYCLC RLPYDVTRFM IECDMCQDWF HGSCVGVEEE KAADIDLYHC PNCEVLHGPS 

        70         80         90        100        110        120 
IMKKRRGSSK GHDNHKGKPL KTGSSMFIRE LRGRTFDSSD EVILKPTGSQ LTVEFLEENS 

       130        140        150        160        170        180 
FSVPILVLKK DGLGMTLPSP SFTVRDVEHY VGSDKEIDVI DVARQADCKM KLGDFVKYYY 

       190        200        210        220        230        240 
SGKREKVLNV ISLEFSDTRL SNLVETPRIV RKLSWVENLW PEECVFERPN VQKYCLMSVR 

       250        260        270        280        290        300 
DSYTDFHIDF GGTSVWYHVL KGEKIFYLIR PTNANLTLFE CWSSSSNQNE MFFGDQVEKC 

       310        320        330        340        350        360 
YKCSVKQGQT LFIPTGWIHA VLTPVDCLAF GGNFLHSLNI EMQLKAYEIE KRLSTADLFK 

       370        380        390        400        410        420 
FPNFETICWY VGKHILDIFR GLRENRRHPA SYLVHGGKAL NLAFRAWTKK EALPDHEDEI 

       430        440        450        460        470        480 
PETVRTVQLI KDLAREIRLV EDIFQQNVGK TSNIFGLQRI FPAGSIPLTK PAHSTSVSMS 

       490        500        510        520        530        540 
KLSLPSKNGS KKKGLKPKDI FKKAERKGKQ SSALGPAGQL SYNLMDPYSH QALKTGPSQK 

       550        560        570        580        590        600 
AKFNMSGTSL NDSDDDSADM DLDGSENPLA LLMANGSTKR MKSVSKSRRA KIAKKVDSAR 

       610        620        630        640        650        660 
LVAEQVMGDE FDLDSDDELQ IDERLGKEKA NLLIRSKFPR KLPRAKPCSD PNRIREPGEV 

       670        680        690        700        710        720 
EFDIEEDYTT DEDMVEGVES KLGNGSGAGG ILDLLKASRQ VGGPDYAALT EAPASPSTQE 

       730        740        750        760        770        780 
AIQGMLCMAN LQSSSSSPAT SSLQAWWTGG QERSSGSSSS GLGTVSSSPA SQRTPGKRPI 

       790        800        810        820        830        840 
KRPAYWKNES EEEENASLDE QDSLGACFKD AEYIYPSLES DDDDPALKSR PKKKKNSDDA 

       850        860        870        880        890        900 
PWSPKARVTP TLPKQDRPVR EGTRVASIET GLAAAAAKLA QQELQKAQKK KYIKKKPLLK 

       910        920        930        940        950        960 
EVEQPRPQDS NPIMTMPAPT VATTPQPDTS SSPQPPPEPK QEALSGSLAD HEYTARPNAF 

       970        980        990       1000       1010       1020 
GMAQANRSTT PMAPGVFLTQ RRPSVGSQSS QAGQGKRPKK GLATAKQRLG RILKIHRNGK 


LLL 

« Hide

Isoform 2 [UniParc].

Checksum: E14CF1810F1D3492
Show »

FASTA79588,919
Isoform 3 [UniParc].

Checksum: A0A47C4A877F9291
Show »

FASTA46453,421

References

« Hide 'large scale' references
[1]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-490 (ISOFORM 1).
Strain: C57BL/6J.
Tissue: Bone.
[2]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C57BL/6J.
[3]"Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 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., Aizawa H., Yuasa S., Nakajima D., Nagase T., Ohara O., Koga H.
DNA Res. 10:35-48(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 19-1023 (ISOFORM 1).
Tissue: Brain.
[4]"Gene content of the 750-kb critical region for mouse embryonic ectoderm lethal tcl-w5."
Abe K., Yuzuriha M., Sugimoto M., Ko M.S., Brathwaite M.E., Waeltz P., Nagaraja R.
Mamm. Genome 15:265-276(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-899.
Strain: 129/Sv.
[5]"Large-scale phosphorylation analysis of mouse liver."
Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-820, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Liver.
[6]"The phagosomal proteome in interferon-gamma-activated macrophages."
Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-615 AND SER-820, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Solution structure of PHD domain in protein AA017385."
RIKEN structural genomics initiative (RSGI)
Submitted (JUL-2002) to the EMBL/GenBank/DDBJ databases
Cited for: STRUCTURE BY NMR OF 1-66.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK036609 mRNA. Translation: BAC29505.1.
AK040943 mRNA. Translation: BAC30755.2.
AK040969 mRNA. Translation: BAC30763.1.
AL662922 Genomic DNA. Translation: CAM17161.1.
AL840642, AL662922 Genomic DNA. Translation: CAM15464.1.
AL662922, AL840642 Genomic DNA. Translation: CAM17159.1.
AL662922 Genomic DNA. Translation: CAM17163.1. Sequence problems.
AK122447 mRNA. Translation: BAC65729.1.
AF528164 Genomic DNA. Translation: AAO17385.1. Sequence problems.
CCDSCCDS30470.1. [Q80TJ7-2]
CCDS53223.1. [Q80TJ7-1]
RefSeqNP_001009544.1. NM_001009544.2.
NP_001106825.1. NM_001113354.1. [Q80TJ7-1]
NP_796175.1. NM_177201.5. [Q80TJ7-2]
XP_006528938.1. XM_006528875.1. [Q80TJ7-1]
XP_006528939.1. XM_006528876.1. [Q80TJ7-1]
XP_006528940.1. XM_006528877.1. [Q80TJ7-1]
XP_006528943.1. XM_006528880.1. [Q80TJ7-1]
UniGeneMm.17156.
Mm.84774.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WEPNMR-A1-63[»]
ProteinModelPortalQ80TJ7.
SMRQ80TJ7. Positions 3-447.
ModBaseSearch...
MobiDBSearch...

Chemistry

ChEMBLCHEMBL3038497.

PTM databases

PhosphoSiteQ80TJ7.

Proteomic databases

PaxDbQ80TJ7.
PRIDEQ80TJ7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000024121; ENSMUSP00000024121; ENSMUSG00000023350.
ENSMUST00000046950; ENSMUSP00000040765; ENSMUSG00000041229. [Q80TJ7-1]
ENSMUST00000046962; ENSMUSP00000041312; ENSMUSG00000041229. [Q80TJ7-2]
ENSMUST00000112662; ENSMUSP00000108281; ENSMUSG00000041229. [Q80TJ7-2]
ENSMUST00000112666; ENSMUSP00000108285; ENSMUSG00000041229. [Q80TJ7-3]
ENSMUST00000168501; ENSMUSP00000127653; ENSMUSG00000041229. [Q80TJ7-1]
GeneID320595.
74042.
KEGGmmu:320595.
mmu:74042.
UCSCuc009upd.1. mouse. [Q80TJ7-3]
uc009upe.1. mouse. [Q80TJ7-1]

Organism-specific databases

CTD23133.
MGIMGI:2444341. Phf8.
RougeSearch...

Phylogenomic databases

eggNOGNOG290496.
GeneTreeENSGT00550000074396.
HOVERGENHBG045631.
InParanoidA2ABU8.
KOK11445.
OMAEIDLYHC.
OrthoDBEOG73JKV9.
PhylomeDBQ80TJ7.
TreeFamTF106480.

Gene expression databases

ArrayExpressQ80TJ7.
BgeeQ80TJ7.
CleanExMM_PHF8.
GenevestigatorQ80TJ7.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR003347. 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]
PfamPF02373. JmjC. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ80TJ7.
NextBio339610.
PROQ80TJ7.
SOURCESearch...

Entry information

Entry namePHF8_MOUSE
AccessionPrimary (citable) accession number: Q80TJ7
Secondary accession number(s): A2ABU8 expand/collapse secondary AC list , A2ABV0, A2ABV2, Q8BLX8, Q8BLY0, Q8BZ61, Q8CG26
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: August 16, 2005
Last modified: July 9, 2014
This is version 95 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot