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Protein

Lysine-specific demethylase 4C

Gene

Kdm4c

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate (By similarity).By similarity

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei1342-oxoglutarateBy similarity1
Metal bindingi190Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi192Iron; catalyticPROSITE-ProRule annotation1
Binding sitei2002-oxoglutarateBy similarity1
Binding sitei2082-oxoglutarateBy similarity1
Metal bindingi236ZincBy similarity1
Metal bindingi242ZincBy similarity1
Binding sitei2432-oxoglutarateBy similarity1
Metal bindingi278Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi308ZincBy similarity1
Metal bindingi310ZincBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri687 – 745PHD-type 1Add BLAST59
Zinc fingeri750 – 783C2HC pre-PHD-typePROSITE-ProRule annotationAdd BLAST34
Zinc fingeri806 – 863PHD-type 2PROSITE-ProRule annotationAdd BLAST58

GO - Molecular functioni

  • androgen receptor binding Source: BHF-UCL
  • chromatin binding Source: Ensembl
  • enzyme binding Source: BHF-UCL
  • histone demethylase activity Source: MGI
  • histone demethylase activity (H3-K36 specific) Source: MGI
  • histone demethylase activity (H3-K9 specific) Source: UniProtKB
  • zinc ion binding Source: MGI

GO - Biological processi

  • blastocyst formation Source: MGI
  • histone H3-K36 demethylation Source: MGI
  • histone H3-K9 demethylation Source: MGI
  • negative regulation of histone H3-K9 trimethylation Source: MGI
  • positive regulation of cell proliferation Source: MGI
  • positive regulation of gene expression Source: Ensembl
  • positive regulation of neuron differentiation Source: Ensembl
  • regulation of gene expression Source: MGI
  • regulation of stem cell differentiation Source: MGI
  • regulation of stem cell population maintenance Source: MGI
  • regulation of transcription from RNA polymerase II promoter Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

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

Enzyme and pathway databases

ReactomeiR-MMU-3214842. HDMs demethylate histones.
R-MMU-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 4C (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 3C
Jumonji domain-containing protein 2C
Gene namesi
Name:Kdm4c
Synonyms:Jhdm3c, Jmjd2c, Kiaa0780
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:1924054. Kdm4c.

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

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001831781 – 1054Lysine-specific demethylase 4CAdd BLAST1054

Proteomic databases

EPDiQ8VCD7.
MaxQBiQ8VCD7.
PaxDbiQ8VCD7.
PeptideAtlasiQ8VCD7.
PRIDEiQ8VCD7.

PTM databases

iPTMnetiQ8VCD7.
PhosphoSitePlusiQ8VCD7.

Expressioni

Gene expression databases

BgeeiENSMUSG00000028397.
CleanExiMM_JMJD2C.
ExpressionAtlasiQ8VCD7. baseline and differential.
GenevisibleiQ8VCD7. MM.

Interactioni

GO - Molecular functioni

  • androgen receptor binding Source: BHF-UCL
  • enzyme binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi218326. 9 interactors.
STRINGi10090.ENSMUSP00000030102.

Structurei

3D structure databases

ProteinModelPortaliQ8VCD7.
SMRiQ8VCD7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini16 – 58JmjNPROSITE-ProRule annotationAdd BLAST43
Domaini144 – 310JmjCPROSITE-ProRule annotationAdd BLAST167
Domaini875 – 932Tudor 1Add BLAST58
Domaini933 – 989Tudor 2Add BLAST57

Domaini

The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails (By similarity).By similarity

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri687 – 745PHD-type 1Add BLAST59
Zinc fingeri750 – 783C2HC pre-PHD-typePROSITE-ProRule annotationAdd BLAST34
Zinc fingeri806 – 863PHD-type 2PROSITE-ProRule annotationAdd BLAST58

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ8VCD7.
KOiK06709.
OMAiQIAMKRE.
OrthoDBiEOG091G01FR.
PhylomeDBiQ8VCD7.
TreeFamiTF106449.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
InterProiView protein in InterPro
IPR034732. EPHD.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
PfamiView protein in Pfam
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
SMARTiView protein in SMART
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiView protein in PROSITE
PS51805. EPHD. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8VCD7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEVVEVESPL NPSCKIMTFR PSMEEFREFN KYLAYMESKG AHRAGLAKVI
60 70 80 90 100
PPKEWKPRQC YDDIDNLLIP APIQQMVTGQ SGLFTQYNIQ KKAMTVKEFR
110 120 130 140 150
QLANSSKYCT PRYLDYEDLE RKYWKNLTFV APIYGADING SIYDEGVDEW
160 170 180 190 200
NIARLNTVLD VVEEECGISI EGVNTPYLYF GMWKTTFAWH TEDMDLYSIN
210 220 230 240 250
YLHFGEPKSW YAIPPEHGKR LERLAQGFFP SSSQGCDAFL RHKMTLISPS
260 270 280 290 300
VLKKYGIPFD KITQEAGEFM ITFPYGYHAG FNHGFNCAES TNFATVRWID
310 320 330 340 350
YGKVAKLCTC RNDMVKISMD IFVKKFQPDR YQIWKQGKDI YTIDHTKPTP
360 370 380 390 400
ESTPEVKTWL QRKKKLRKPP KSLQGNKPLC KRPKPEEDEE FAEFSGEEGA
410 420 430 440 450
NPAMGPRHLK VTEKPEKALK LGKLEESSAK EALDTRIQVD QSLLNDTKLS
460 470 480 490 500
GKGCISSSVT AEIPPEDNRA SAVISPSQLK EGADCIPLSH GHQAGKESHL
510 520 530 540 550
LKILKLESPK IPSPLPESNK VLTEGEENDE EGHGSNLEPG EIPEALSEER
560 570 580 590 600
NGLNIPKIIE GQPKTTKSWR HPLGKPPARS PMTLVKQQVA SDEELPEVLS
610 620 630 640 650
IDEEVEETES WAKPLIHLWQ TKSPNFMAEQ EYNATVAKME PNCAICTLLM
660 670 680 690 700
PYYKPDSSKE ENDSRWETAV NEVVQSGRKT KPIIPEMCFI YSEENVDYSP
710 720 730 740 750
PNAFLEEDGT SLLISCAKCF VRVHASCYGV PSHEVCDGWL CARCKRNAWT
760 770 780 790 800
AECCLCNLRG GALKQTKNNQ WAHVICAVAV PEVRFTNVPE RTQIDVDRIP
810 820 830 840 850
LQRLKLKCIF CRHRVKKVSG ACIQCSYGRC PASFHVTCAH AAGVLMEPDD
860 870 880 890 900
WPYVVNITCF RHRVNSNAKS KTCEKAISVG QTVITKHRNT RYYSCRVIDV
910 920 930 940 950
TSQTFYEVMF DDGSFSRDTF PEDIVSRNCV KLGPPAEGEV IQVKWPDGKL
960 970 980 990 1000
YGAKYLGSNV AYMYQVEFED GSQIAMKRED IYTLDEELPK RVKARFSTAS
1010 1020 1030 1040 1050
DMRFEDTFYG ADVIQGERKR QRVLSSRLKN EYVDDPVYRT FLKSSFQKKC

QKRQ
Length:1,054
Mass (Da):119,966
Last modified:March 1, 2002 - v1
Checksum:i86F275FC428B8EDA
GO

Sequence cautioni

The sequence BAD32301 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti300D → V in BAC35267 (PubMed:16141072).Curated1
Sequence conflicti687M → V in BAE25700 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK173023 mRNA. Translation: BAD32301.1. Different initiation.
AK053104 mRNA. Translation: BAC35267.1.
AK081769 mRNA. Translation: BAC38327.1.
AK144103 mRNA. Translation: BAE25700.1.
BC020180 mRNA. Translation: AAH20180.1.
BC042424 mRNA. Translation: AAH42424.1.
CCDSiCCDS18287.1.
RefSeqiNP_001165566.1. NM_001172095.1.
NP_659036.1. NM_144787.2.
XP_006538415.1. XM_006538352.3.
UniGeneiMm.209059.

Genome annotation databases

EnsembliENSMUST00000030102; ENSMUSP00000030102; ENSMUSG00000028397.
ENSMUST00000077851; ENSMUSP00000077017; ENSMUSG00000028397.
GeneIDi76804.
KEGGimmu:76804.
UCSCiuc008tjj.2. mouse.

Similar proteinsi

Entry informationi

Entry nameiKDM4C_MOUSE
AccessioniPrimary (citable) accession number: Q8VCD7
Secondary accession number(s): Q3UNP7
, Q69ZZ5, Q8BUY6, Q8BWA1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: March 1, 2002
Last modified: August 30, 2017
This is version 125 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, 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