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Q9UPP1

- PHF8_HUMAN

UniProt

Q9UPP1 - PHF8_HUMAN

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Protein

Histone lysine demethylase PHF8

Gene

PHF8

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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. Only has activity toward H4K20Me1 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 H3K4me3.10 Publications

Catalytic activityi

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.

Cofactori

Binds 1 Fe2+ ion per subunit.2 Publications

Kineticsi

  1. KM=134 µM for histone H3 H3K9Me21 Publication
  2. KM=8 µM for histone H3 H3K4me3 and H3K9Me21 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei280 – 2801Substrate
Metal bindingi283 – 2831Iron; catalytic2 PublicationsPROSITE-ProRule annotation
Metal bindingi285 – 2851Iron; catalytic2 PublicationsPROSITE-ProRule annotation
Binding sitei300 – 3001Substrate
Metal bindingi355 – 3551Iron; catalytic2 PublicationsPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri41 – 9252PHD-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. chromatin binding Source: UniProtKB
  2. histone demethylase activity Source: UniProtKB
  3. histone demethylase activity (H3-K27 specific) Source: UniProtKB
  4. histone demethylase activity (H3-K36 specific) Source: UniProtKB
  5. histone demethylase activity (H3-K9 specific) Source: UniProtKB
  6. histone demethylase activity (H4-K20 specific) Source: UniProtKB
  7. iron ion binding Source: UniProtKB
  8. methylated histone binding Source: UniProtKB
  9. 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 Source: UniProtKB
  10. zinc ion binding Source: UniProtKB

GO - Biological processi

  1. brain development Source: UniProtKB
  2. G1/S transition of mitotic cell cycle Source: UniProtKB
  3. histone H3-K27 demethylation Source: UniProtKB
  4. histone H3-K36 demethylation Source: UniProtKB
  5. histone H3-K9 demethylation Source: UniProtKB
  6. histone H4-K20 demethylation Source: UniProtKB
  7. mitotic cell cycle Source: Reactome
  8. negative regulation of chromatin silencing at rDNA Source: UniProtKB
  9. positive regulation of transcription, DNA-templated Source: UniProtKB
  10. positive regulation of transcription from RNA polymerase I promoter Source: UniProtKB
  11. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Cell cycle, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_172744. Condensation of Prophase Chromosomes.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone lysine demethylase PHF8 (EC:1.14.11.27)
Alternative name(s):
PHD finger protein 8
Gene namesi
Name:PHF8
Synonyms:KIAA1111, ZNF422
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome X

Organism-specific databases

HGNCiHGNC:20672. PHF8.

Subcellular locationi

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

GO - Cellular componenti

  1. microtubule cytoskeleton Source: HPA
  2. nucleolus Source: UniProtKB
  3. nucleoplasm Source: Reactome
  4. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked, syndromic, Siderius type (MRXSSD) [MIM:300263]: A syndrome characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.2 Publications
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti315 – 3151F → S in MRXSSD; abolishes histone methyltransferase activity. 1 Publication
VAR_062250

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi43 – 431Y → A: Abolishes binding to H3K4me3; when associated with A-50. 2 Publications
Mutagenesisi50 – 501Y → A: Abolishes binding to H3K4me3; when associated with A-43. Abolishes binding to H3K4me3; when associated with A-65. 1 Publication
Mutagenesisi65 – 651W → A: Abolishes binding to H3K4me3; when associated with A-50. 1 Publication
Mutagenesisi69 – 691S → A: Impairs phosphorylation by CDK1 and dissociation from chromatin when cells enter mitosis; when associated with A-120. 1 Publication
Mutagenesisi120 – 1201S → A: Impairs phosphorylation by CDK1 and dissociation from chromatin when cells enter mitosis; when associated with A-69. 1 Publication
Mutagenesisi283 – 2853HID → AAA: Abolishes histone methyltransferase activity. 1 Publication
Mutagenesisi283 – 2831H → A: Abolishes histone methyltransferase activity. 3 Publications

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

MIMi300263. phenotype.
Orphaneti85287. X-linked intellectual disability, Siderius type.
PharmGKBiPA134889361.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10601060Histone lysine demethylase PHF8PRO_0000059295Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei69 – 691Phosphoserine; by CDK11 Publication
Modified residuei120 – 1201Phosphoserine; by CDK11 Publication
Modified residuei651 – 6511Phosphoserine1 Publication
Modified residuei705 – 7051Phosphothreonine2 Publications
Modified residuei706 – 7061Phosphothreonine2 Publications
Modified residuei804 – 8041Phosphoserine1 Publication
Modified residuei854 – 8541Phosphoserine3 Publications
Modified residuei857 – 8571Phosphoserine5 Publications
Modified residuei880 – 8801Phosphoserine3 Publications

Post-translational modificationi

Phosphorylation at Ser-69 and Ser-120 are required for dissociation from chromatin and accumulation of H4K20Me1 levels during prophase.6 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9UPP1.
PaxDbiQ9UPP1.
PRIDEiQ9UPP1.

PTM databases

PhosphoSiteiQ9UPP1.

Expressioni

Gene expression databases

BgeeiQ9UPP1.
CleanExiHS_PHF8.
ExpressionAtlasiQ9UPP1. baseline and differential.
GenevestigatoriQ9UPP1.

Organism-specific databases

HPAiHPA038779.

Interactioni

Subunit structurei

Interacts with POLR1B, UBTF, SETD1A, HCFC1, E2F1 and ZNF711.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PML-RARQ151566EBI-6601215,EBI-867256
RARAP102762EBI-6601215,EBI-413374

Protein-protein interaction databases

BioGridi116751. 34 interactions.
DIPiDIP-38913N.
IntActiQ9UPP1. 3 interactions.
MINTiMINT-4651164.
STRINGi9606.ENSP00000338868.

Structurei

Secondary structure

1
1060
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni44 – 474Combined sources
Beta strandi56 – 583Combined sources
Turni60 – 623Combined sources
Beta strandi65 – 673Combined sources
Helixi68 – 714Combined sources
Helixi75 – 784Combined sources
Beta strandi81 – 833Combined sources
Helixi87 – 937Combined sources
Helixi121 – 1299Combined sources
Turni136 – 1383Combined sources
Turni144 – 1463Combined sources
Helixi149 – 1557Combined sources
Beta strandi161 – 1655Combined sources
Turni167 – 1704Combined sources
Helixi180 – 1878Combined sources
Beta strandi192 – 1976Combined sources
Turni198 – 2014Combined sources
Beta strandi202 – 2076Combined sources
Helixi208 – 2158Combined sources
Beta strandi224 – 2307Combined sources
Helixi235 – 2384Combined sources
Helixi244 – 2496Combined sources
Helixi251 – 2555Combined sources
Beta strandi270 – 2745Combined sources
Beta strandi278 – 2836Combined sources
Helixi286 – 2883Combined sources
Beta strandi290 – 30516Combined sources
Helixi309 – 31911Combined sources
Helixi324 – 3263Combined sources
Helixi329 – 3313Combined sources
Beta strandi332 – 3343Combined sources
Beta strandi337 – 3426Combined sources
Beta strandi346 – 3494Combined sources
Beta strandi354 – 37017Combined sources
Beta strandi373 – 3753Combined sources
Helixi376 – 38914Combined sources
Helixi393 – 3953Combined sources
Helixi400 – 42021Combined sources
Helixi427 – 44418Combined sources
Turni446 – 4483Combined sources
Helixi449 – 4513Combined sources
Helixi453 – 4553Combined sources
Helixi462 – 47716Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WWUX-ray2.15A115-483[»]
3K3NX-ray2.40A122-483[»]
3K3OX-ray2.10A122-483[»]
3KV4X-ray2.19A37-483[»]
4DO0X-ray2.55A115-483[»]
ProteinModelPortaliQ9UPP1.
SMRiQ9UPP1. Positions 39-483.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UPP1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini231 – 387157JmjCPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni101 – 11515LinkerAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi769 – 80739Ser-richAdd
BLAST

Domaini

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

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 fingeri41 – 9252PHD-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG290496.
GeneTreeiENSGT00550000074396.
HOGENOMiHOG000231232.
HOVERGENiHBG045631.
InParanoidiQ9UPP1.
KOiK11445.
OMAiEIDLYHC.
PhylomeDBiQ9UPP1.
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]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9UPP1-1) [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
MNRSRAIVQR GRVLPPPAPL DTTNLAGRRT LQGRAKMASV PVYCLCRLPY
60 70 80 90 100
DVTRFMIECD MCQDWFHGSC VGVEEEKAAD IDLYHCPNCE VLHGPSIMKK
110 120 130 140 150
RRGSSKGHDT HKGKPVKTGS PTFVRELRSR TFDSSDEVIL KPTGNQLTVE
160 170 180 190 200
FLEENSFSVP ILVLKKDGLG MTLPSPSFTV RDVEHYVGSD KEIDVIDVTR
210 220 230 240 250
QADCKMKLGD FVKYYYSGKR EKVLNVISLE FSDTRLSNLV ETPKIVRKLS
260 270 280 290 300
WVENLWPEEC VFERPNVQKY CLMSVRDSYT DFHIDFGGTS VWYHVLKGEK
310 320 330 340 350
IFYLIRPTNA NLTLFECWSS SSNQNEMFFG DQVDKCYKCS VKQGQTLFIP
360 370 380 390 400
TGWIHAVLTP VDCLAFGGNF LHSLNIEMQL KAYEIEKRLS TADLFRFPNF
410 420 430 440 450
ETICWYVGKH ILDIFRGLRE NRRHPASYLV HGGKALNLAF RAWTRKEALP
460 470 480 490 500
DHEDEIPETV RTVQLIKDLA REIRLVEDIF QQNVGKTSNI FGLQRIFPAG
510 520 530 540 550
SIPLTRPAHS TSVSMSRLSL PSKNGSKKKG LKPKELFKKA ERKGKESSAL
560 570 580 590 600
GPAGQLSYNL MDTYSHQALK TGSFQKAKFN ITGACLNDSD DDSPDLDLDG
610 620 630 640 650
NESPLALLMS NGSTKRVKSL SKSRRTKIAK KVDKARLMAE QVMEDEFDLD
660 670 680 690 700
SDDELQIDER LGKEKATLII RPKFPRKLPR AKPCSDPNRV REPGEVEFDI
710 720 730 740 750
EEDYTTDEDM VEGVEGKLGN GSGAGGILDL LKASRQVGGP DYAALTEAPA
760 770 780 790 800
SPSTQEAIQG MLCMANLQSS SSSPATSSLQ AWWTGGQDRS SGSSSSGLGT
810 820 830 840 850
VSNSPASQRT PGKRPIKRPA YWRTESEEEE ENASLDEQDS LGACFKDAEY
860 870 880 890 900
IYPSLESDDD DPALKSRPKK KKNSDDAPWS PKARVTPTLP KQDRPVREGT
910 920 930 940 950
RVASIETGLA AAAAKLAQQE LQKAQKKKYI KKKPLLKEVE QPRPQDSNLS
960 970 980 990 1000
LTVPAPTVAA TPQLVTSSSP LPPPEPKQEA LSGSLADHEY TARPNAFGMA
1010 1020 1030 1040 1050
QANRSTTPMA PGVFLTQRRP SVGSQSNQAG QGKRPKKGLA TAKQRLGRIL
1060
KIHRNGKLLL
Length:1,060
Mass (Da):117,864
Last modified:August 16, 2005 - v3
Checksum:i04C83D7C5E9E56B8
GO
Isoform 2 (identifier: Q9UPP1-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.

Show »
Length:1,024
Mass (Da):113,913
Checksum:i75773C0918578FB0
GO
Isoform 3 (identifier: Q9UPP1-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     478-578: Missing.

Note: No experimental confirmation available.

Show »
Length:959
Mass (Da):106,902
Checksum:iF54BE8A814BF1701
GO
Isoform 4 (identifier: Q9UPP1-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.
     478-578: Missing.
     1060-1060: L → LRQVIVQAECRQAIHEPKLKRRDAHP

Note: No experimental confirmation available.

Show »
Length:948
Mass (Da):105,913
Checksum:iF32740CB7A2CE3F6
GO
Isoform 5 (identifier: Q9UPP1-5) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.
     717-746: KLGNGSGAGGILDLLKASRQVGGPDYAALT → YQTATPAPAQGAS
     920-931: ELQKAQKKKYIK → VKKMKLSLTDSG
     932-1060: Missing.

Show »
Length:878
Mass (Da):98,290
Checksum:i690CE764C0C28D28
GO

Sequence cautioni

The sequence BAA83063.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.
The sequence BAB13877.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
The sequence CAI45929.1 differs from that shown. Reason: Erroneous termination at position 419. Translated as Arg.

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti232 – 2321S → P in BAB13877. (PubMed:12168954)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti315 – 3151F → S in MRXSSD; abolishes histone methyltransferase activity. 1 Publication
VAR_062250

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 3636Missing in isoform 2, isoform 4 and isoform 5. 3 PublicationsVSP_014964Add
BLAST
Alternative sequencei478 – 578101Missing in isoform 3 and isoform 4. 1 PublicationVSP_014965Add
BLAST
Alternative sequencei717 – 74630KLGNG…YAALT → YQTATPAPAQGAS in isoform 5. 1 PublicationVSP_054019Add
BLAST
Alternative sequencei920 – 93112ELQKA…KKYIK → VKKMKLSLTDSG in isoform 5. 1 PublicationVSP_054020Add
BLAST
Alternative sequencei932 – 1060129Missing in isoform 5. 1 PublicationVSP_054021Add
BLAST
Alternative sequencei1060 – 10601L → LRQVIVQAECRQAIHEPKLK RRDAHP in isoform 4. 1 PublicationVSP_043640

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB029034 mRNA. Translation: BAA83063.1. Different initiation.
CR933612 mRNA. Translation: CAI45929.1. Sequence problems.
AK021696 mRNA. Translation: BAB13877.1. Different initiation.
AK022788 mRNA. Translation: BAG51116.1.
AK304272 mRNA. Translation: BAH14147.1.
AL589872 Genomic DNA. No translation available.
AL732374 Genomic DNA. No translation available.
Z98051 Genomic DNA. No translation available.
BC042108 mRNA. No translation available.
BC053861 mRNA. Translation: AAH53861.1.
CCDSiCCDS14355.1. [Q9UPP1-2]
CCDS55418.1. [Q9UPP1-4]
CCDS55419.1. [Q9UPP1-5]
CCDS55420.1. [Q9UPP1-1]
RefSeqiNP_001171825.1. NM_001184896.1. [Q9UPP1-1]
NP_001171826.1. NM_001184897.1. [Q9UPP1-4]
NP_055922.1. NM_015107.2. [Q9UPP1-2]
UniGeneiHs.133352.

Genome annotation databases

EnsembliENST00000322659; ENSP00000319473; ENSG00000172943. [Q9UPP1-5]
ENST00000338154; ENSP00000338868; ENSG00000172943. [Q9UPP1-2]
ENST00000338946; ENSP00000340051; ENSG00000172943. [Q9UPP1-4]
ENST00000357988; ENSP00000350676; ENSG00000172943. [Q9UPP1-1]
GeneIDi23133.
KEGGihsa:23133.
UCSCiuc004dst.3. human. [Q9UPP1-1]
uc004dsw.3. human. [Q9UPP1-4]

Polymorphism databases

DMDMi73620986.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB029034 mRNA. Translation: BAA83063.1 . Different initiation.
CR933612 mRNA. Translation: CAI45929.1 . Sequence problems.
AK021696 mRNA. Translation: BAB13877.1 . Different initiation.
AK022788 mRNA. Translation: BAG51116.1 .
AK304272 mRNA. Translation: BAH14147.1 .
AL589872 Genomic DNA. No translation available.
AL732374 Genomic DNA. No translation available.
Z98051 Genomic DNA. No translation available.
BC042108 mRNA. No translation available.
BC053861 mRNA. Translation: AAH53861.1 .
CCDSi CCDS14355.1. [Q9UPP1-2 ]
CCDS55418.1. [Q9UPP1-4 ]
CCDS55419.1. [Q9UPP1-5 ]
CCDS55420.1. [Q9UPP1-1 ]
RefSeqi NP_001171825.1. NM_001184896.1. [Q9UPP1-1 ]
NP_001171826.1. NM_001184897.1. [Q9UPP1-4 ]
NP_055922.1. NM_015107.2. [Q9UPP1-2 ]
UniGenei Hs.133352.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2WWU X-ray 2.15 A 115-483 [» ]
3K3N X-ray 2.40 A 122-483 [» ]
3K3O X-ray 2.10 A 122-483 [» ]
3KV4 X-ray 2.19 A 37-483 [» ]
4DO0 X-ray 2.55 A 115-483 [» ]
ProteinModelPortali Q9UPP1.
SMRi Q9UPP1. Positions 39-483.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 116751. 34 interactions.
DIPi DIP-38913N.
IntActi Q9UPP1. 3 interactions.
MINTi MINT-4651164.
STRINGi 9606.ENSP00000338868.

Chemistry

BindingDBi Q9UPP1.
ChEMBLi CHEMBL1938212.
GuidetoPHARMACOLOGYi 2698.

PTM databases

PhosphoSitei Q9UPP1.

Polymorphism databases

DMDMi 73620986.

Proteomic databases

MaxQBi Q9UPP1.
PaxDbi Q9UPP1.
PRIDEi Q9UPP1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000322659 ; ENSP00000319473 ; ENSG00000172943 . [Q9UPP1-5 ]
ENST00000338154 ; ENSP00000338868 ; ENSG00000172943 . [Q9UPP1-2 ]
ENST00000338946 ; ENSP00000340051 ; ENSG00000172943 . [Q9UPP1-4 ]
ENST00000357988 ; ENSP00000350676 ; ENSG00000172943 . [Q9UPP1-1 ]
GeneIDi 23133.
KEGGi hsa:23133.
UCSCi uc004dst.3. human. [Q9UPP1-1 ]
uc004dsw.3. human. [Q9UPP1-4 ]

Organism-specific databases

CTDi 23133.
GeneCardsi GC0XM053979.
HGNCi HGNC:20672. PHF8.
HPAi HPA038779.
MIMi 300263. phenotype.
300560. gene.
neXtProti NX_Q9UPP1.
Orphaneti 85287. X-linked intellectual disability, Siderius type.
PharmGKBi PA134889361.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG290496.
GeneTreei ENSGT00550000074396.
HOGENOMi HOG000231232.
HOVERGENi HBG045631.
InParanoidi Q9UPP1.
KOi K11445.
OMAi EIDLYHC.
PhylomeDBi Q9UPP1.
TreeFami TF106480.

Enzyme and pathway databases

Reactomei REACT_172744. Condensation of Prophase Chromosomes.

Miscellaneous databases

ChiTaRSi PHF8. human.
EvolutionaryTracei Q9UPP1.
GeneWikii PHF8.
GenomeRNAii 23133.
NextBioi 35468941.
PROi Q9UPP1.
SOURCEi Search...

Gene expression databases

Bgeei Q9UPP1.
CleanExi HS_PHF8.
ExpressionAtlasi Q9UPP1. baseline and differential.
Genevestigatori Q9UPP1.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
InterProi 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.
[Graphical view ]
Pfami PF02373. JmjC. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view ]
SMARTi SM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view ]
SUPFAMi SSF57903. SSF57903. 1 hit.
PROSITEi PS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 6:197-205(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  2. "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
    Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
    DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION.
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 34-927 (ISOFORM 3), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 515-1060 (ISOFORM 1).
    Tissue: Embryo, Teratocarcinoma and Trachea.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Endometrial tumor.
  5. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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] (ISOFORMS 2 AND 5).
    Tissue: Brain and Cervix.
  7. Cited for: INVOLVEMENT IN MRXSSD.
  8. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-857, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-705; THR-706; SER-854; SER-857 AND SER-880, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  10. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-651; THR-705; THR-706; SER-854 AND SER-857, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  12. "PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis."
    Zhu Z., Wang Y., Li X., Wang Y., Xu L., Wang X., Sun T., Dong X., Chen L., Mao H., Yu Y., Li J., Chen P.A., Chen C.D.
    Cell Res. 20:794-801(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF HIS-283.
  13. "The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation."
    Qiu J., Shi G., Jia Y., Li J., Wu M., Li J., Dong S., Wong J.
    Cell Res. 20:908-918(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CHARACTERIZATION OF VARIANT MRXSSD SER-315.
  14. "PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase."
    Loenarz C., Ge W., Coleman M.L., Rose N.R., Cooper C.D.O., Klose R.J., Ratcliffe P.J., Schofield C.J.
    Hum. Mol. Genet. 19:217-222(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBCELLULAR LOCATION.
  15. "A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation."
    Kleine-Kohlbrecher D., Christensen J., Vandamme J., Abarrategui I., Bak M., Tommerup N., Shi X., Gozani O., Rappsilber J., Salcini A.E., Helin K.
    Mol. Cell 38:165-178(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN PHD-FINGER, INTERACTION WITH ZNF711, CHARACTERIZATION OF VARIANT MRXSSD SER-315, MUTAGENESIS OF HIS-283.
  16. "PHF8 targets histone methylation and RNA polymerase II to activate transcription."
    Fortschegger K., de Graaf P., Outchkourov N.S., van Schaik F.M., Timmers H.T., Shiekhattar R.
    Mol. Cell. Biol. 30:3286-3298(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN PHD-FINGER, CHARACTERIZATION OF VARIANT MRXSSD SER-315.
  17. "PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation."
    Feng W., Yonezawa M., Ye J., Jenuwein T., Grummt I.
    Nat. Struct. Mol. Biol. 17:445-450(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH POLR1B AND UBTF, CHARACTERIZATION OF VARIANT MRXSSD SER-315, MUTAGENESIS OF TYR-43 AND 283-HIS--ASP-285.
  18. Cited for: FUNCTION, DOMAIN PHD-FINGER, CHARACTERIZATION OF VARIANT MRXSSD SER-315, MUTAGENESIS OF TYR-43; TYR-50 AND TRP-65.
  19. Cited for: FUNCTION, SUBCELLULAR LOCATION, DOMAIN PHD-FINGER, INTERACTION WITH SETD1A; HCFC1 AND E2F1, CHARACTERIZATION OF VARIANT MRXSSD SER-315, PHOSPHORYLATION AT SER-69 AND SER-120, MUTAGENESIS OF SER-69; SER-120 AND HIS-283.
  20. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-804; SER-857 AND SER-880, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  21. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  22. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-854; SER-857 AND SER-880, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  23. "Structural insights into a novel histone demethylase PHF8."
    Yu L., Wang Y., Huang S., Wang J., Deng Z., Zhang Q., Wu W., Zhang X., Liu Z., Gong W., Chen Z.
    Cell Res. 20:166-173(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 122-483 IN COMPLEX WITH IRON AND ALPHA-KETOGLUTARATE, FUNCTION, CHARACTERIZATION OF VARIANT MRXSSD SER-315.
  24. "Crystal structure of the PHF8 Jumonji domain, an N(epsilon)-methyl lysine demethylase."
    Yue W.W., Hozjan V., Ge W., Loenarz C., Cooper C.D., Schofield C.J., Kavanagh K.L., Oppermann U., McDonough M.A.
    FEBS Lett. 584:825-830(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 115-483.
  25. "Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases."
    Horton J.R., Upadhyay A.K., Qi H.H., Zhang X., Shi Y., Cheng X.
    Nat. Struct. Mol. Biol. 17:38-43(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-447 IN COMPLEX WITH IRON AND N-OXALYLGLYCINE, ZINC-BINDING, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, DOMAIN LINKER AND PHD-FINGER.
  26. "Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate."
    Koivisto A.M., Ala-Mello S., Lemmelae S., Komu H.A., Rautio J., Jaervelae I.
    Clin. Genet. 72:145-149(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT MRXSSD SER-315.

Entry informationi

Entry nameiPHF8_HUMAN
AccessioniPrimary (citable) accession number: Q9UPP1
Secondary accession number(s): B3KMV4
, B7Z911, Q5H9U5, Q5JPR9, Q5JPS0, Q5JPS2, Q5JPS3, Q5VUJ4, Q7Z6D4, Q9HAH2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: August 16, 2005
Last modified: October 29, 2014
This is version 120 of the entry and version 3 of the sequence. [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 X
    Human chromosome X: 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
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3