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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei134 – 1341Alpha-ketoglutarateBy similarity
Metal bindingi190 – 1901Iron; catalyticPROSITE-ProRule annotation
Metal bindingi192 – 1921Iron; catalyticPROSITE-ProRule annotation
Binding sitei200 – 2001Alpha-ketoglutarateBy similarity
Binding sitei208 – 2081Alpha-ketoglutarateBy similarity
Metal bindingi236 – 2361ZincBy similarity
Metal bindingi242 – 2421ZincBy similarity
Metal bindingi278 – 2781Iron; catalyticPROSITE-ProRule annotation
Metal bindingi308 – 3081ZincBy similarity
Metal bindingi310 – 3101ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri687 – 74559PHD-type 1Add
BLAST
Zinc fingeri807 – 86357PHD-type 2Add
BLAST

GO - Molecular functioni

  • androgen receptor binding Source: BHF-UCL
  • dioxygenase activity Source: UniProtKB-KW
  • enzyme binding Source: BHF-UCL
  • histone demethylase activity Source: MGI
  • histone demethylase activity (H3-K9 specific) Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • blastocyst formation Source: MGI
  • histone H3-K9 demethylation Source: UniProtKB
  • negative regulation of histone H3-K9 trimethylation Source: MGI
  • positive regulation of cell proliferation Source: MGI
  • 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
Complete GO annotation...

Keywords - Molecular functioni

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.
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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:1924054. Kdm4c.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • nuclear chromatin Source: MGI
  • pericentric heterochromatin Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10541054Lysine-specific demethylase 4CPRO_0000183178Add
BLAST

Proteomic databases

EPDiQ8VCD7.
MaxQBiQ8VCD7.
PaxDbiQ8VCD7.
PeptideAtlasiQ8VCD7.
PRIDEiQ8VCD7.

PTM databases

iPTMnetiQ8VCD7.
PhosphoSiteiQ8VCD7.

Expressioni

Gene expression databases

BgeeiQ8VCD7.
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 interactions.
STRINGi10090.ENSMUSP00000030102.

Structurei

3D structure databases

ProteinModelPortaliQ8VCD7.
SMRiQ8VCD7. Positions 10-347, 874-992.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini16 – 5843JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini144 – 310167JmjCPROSITE-ProRule annotationAdd
BLAST
Domaini875 – 93258Tudor 1Add
BLAST
Domaini933 – 98957Tudor 2Add
BLAST

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
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.Curated
Contains 2 Tudor domains.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri687 – 74559PHD-type 1Add
BLAST
Zinc fingeri807 – 86357PHD-type 2Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ8VCD7.
KOiK06709.
OMAiDIIQGER.
OrthoDBiEOG7TQV03.
PhylomeDBiQ8VCD7.
TreeFamiTF106449.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]

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 BAD32301.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti300 – 3001D → V in BAC35267 (PubMed:16141072).Curated
Sequence conflicti687 – 6871M → V in BAE25700 (PubMed:16141072).Curated

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_006538352.2.
UniGeneiMm.209059.

Genome annotation databases

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

Cross-referencesi

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_006538352.2.
UniGeneiMm.209059.

3D structure databases

ProteinModelPortaliQ8VCD7.
SMRiQ8VCD7. Positions 10-347, 874-992.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi218326. 9 interactions.
STRINGi10090.ENSMUSP00000030102.

PTM databases

iPTMnetiQ8VCD7.
PhosphoSiteiQ8VCD7.

Proteomic databases

EPDiQ8VCD7.
MaxQBiQ8VCD7.
PaxDbiQ8VCD7.
PeptideAtlasiQ8VCD7.
PRIDEiQ8VCD7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi23081.
MGIiMGI:1924054. Kdm4c.
RougeiSearch...

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ8VCD7.
KOiK06709.
OMAiDIIQGER.
OrthoDBiEOG7TQV03.
PhylomeDBiQ8VCD7.
TreeFamiTF106449.

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.

Miscellaneous databases

PROiQ8VCD7.
SOURCEiSearch...

Gene expression databases

BgeeiQ8VCD7.
CleanExiMM_JMJD2C.
ExpressionAtlasiQ8VCD7. baseline and differential.
GenevisibleiQ8VCD7. MM.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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].
    Tissue: Pancreatic islet.
  2. "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.
    , 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].
    Strain: C3H/HeJ and C57BL/6J.
    Tissue: Brain and Head.
  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: Eye and Salivary gland.
  4. Lubec G., Sunyer B., Chen W.-Q.
    Submitted (JAN-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 815-829, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: OF1.
    Tissue: Hippocampus.

Entry informationi

Entry nameiKDM4C_MOUSE
AccessioniPrimary (citable) accession number: Q8VCD7
Secondary accession number(s): Q3UNP7
, Q69ZZ5, Q8BUY6, Q8BWA1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: March 1, 2002
Last modified: July 6, 2016
This is version 116 of the entry and version 1 of the sequence. [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

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.