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A1YVX4

- KDM5C_PIG

UniProt

A1YVX4 - KDM5C_PIG

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Protein
Lysine-specific demethylase 5C
Gene
KDM5C, JARID1C, SMCX
Organism
Sus scrofa (Pig)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at transcript leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements By similarity.

Cofactori

Alpha-ketoglutarate By similarity.
Binds 1 Fe2+ ion per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi473 – 4731Iron; catalytic By similarity
Metal bindingi476 – 4761Iron; catalytic By similarity
Metal bindingi561 – 5611Iron; catalytic By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri283 – 33351PHD-type 1
Add
BLAST
Zinc fingeri1144 – 120966PHD-type 2
Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. 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: InterPro
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. chromatin modification Source: UniProtKB-KW
  2. regulation of transcription, DNA-templated Source: UniProtKB-KW
  3. 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

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 5C (EC:1.14.11.-)
Alternative name(s):
Histone demethylase JARID1C
Jumonji/ARID domain-containing protein 1C
Protein SmcX
Gene namesi
Name:KDM5C
Synonyms:JARID1C, SMCX
OrganismiSus scrofa (Pig)
Taxonomic identifieri9823 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
ProteomesiUP000008227: Unplaced

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15161516Lysine-specific demethylase 5C
PRO_0000292417Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei276 – 2761Phosphoserine By similarity
Modified residuei1318 – 13181Phosphoserine By similarity

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Part of two distinct complexes, one containing E2F6, and the other containing REST By similarity.

Structurei

3D structure databases

ProteinModelPortaliA1YVX4.
SMRiA1YVX4. Positions 22-147, 278-353.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 5542JmjN
Add
BLAST
Domaini24 – 128105ARID
Add
BLAST
Domaini427 – 593167JmjC
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1413 – 14175Poly-Arg
Compositional biasi1450 – 14578Poly-Glu

Domaini

The first PHD-type zinc finger domain recognizes and binds H3-K9Me3 By similarity.
Both the JmjC domain and the JmjN domain are required for enzymatic activity By similarity.

Sequence similaritiesi

Contains 1 ARID domain.
Contains 1 JmjC domain.
Contains 1 JmjN domain.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG327026.
KOiK11446.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 1 hit.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A1YVX4-1 [UniParc]FASTAAdd to Basket

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MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA     50
DWQPPFAVEV DNFRFTPRIQ RLNELEIVVE EGGYEAICKD RRWARVAQRL 100
NYPPGKNIGS LLRSHYERIV YPYEMYQSGA NLVQCNTRPF DNEEKDKEYK 150
PHSIPLRQSV QPSKFNSYGR RAKRLQPDPE PTEEDIEKNP ELKKLQIYGA 200
GPKMMGLGLM AKDKTLRKKD KEGPECPPTV VVKEESGGDV KVESTSPKTF 250
LESKEELSHS PEPCTKMTMR LRRNHSNAQF IESYVCRMCS RGDEDDKLLL 300
CDGCDDNYHI FCLLPPLPEI PKGVWRCPKC VMAECKRPPE AFGFEQATRE 350
YTLQSFGEMA DSFKADYSNM PVHMVPTELV EKEFWRLVNS IEEDVTVEYG 400
ADIHSKEFGS GFPVSDSKRH LTPEEEEYAT SGWNLNVMPV LEQSVLCHIN 450
ADISGMKVPW LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA 500
AEHLEEVMKK LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG 550
EFVITFPRAY HSGFNQGYNF AEAVNFCTAD WLPAGRQCIE HYRRLRRYCV 600
FSHEELICKM AACPEKLDLN LAAAVHKEMF IMVQEERRLR KALLEKGITE 650
AEREAFELLP DDERQCIKCK TTCFLSALAC YDCPDGLVCL SHINDLCKCS 700
SSRQYLRYRY TLDELPAMLH KLKVRAESFD TWANKVRVAL EVEDGRKRSL 750
EELRALESEA RERRFPNSEL LQRLKNCLSE AEACVSRALG LVSGQEAGPH 800
RVAGLQMTLA ELRAFLDQMN NLPCAMHQIG DVKGILEQVE AYQAEAREAL 850
ASLPSSPGLL QSLLERGRQL GVEVPEAQQL QRQVEQARWL DEVKRTLAPS 900
ARRGTLAVMR GLLVAGASVA PSPAVDKAQA ELQELLTIAE RWEEKAHLCL 950
EARQKHPPAT LEAIIHEAEN IPVHLPNIQA LKEALAKARA WIADVDEIQN 1000
GDHYPCLDDL EGLVAVGRDL PVGLEELRQL ELQVLTAHSW REKASKTFLK 1050
KNSCYTLLEV LCPCADAGSD STKRSRWMEK ELGLYKSDTE LLGLSAQDLR 1100
DPGSVIVAFK EGEQKEKEGI LQLRRTNSAK PSPLASPNTS SSATSICVCG 1150
QVPAGVGALQ CDLCQDWFHG RCVSVPRLLS SPRPSPTSSP LLAWWEWDTK 1200
FLCPLCMRSR RPRLETILAL LVALQRLPVR LPEGEALQCL TERAISWQGR 1250
ARQALAFEDV TALLGRLAEL RQRLQAEPRP EEPPTYPSTP AFDPLREGSG 1300
KDMPKVQGLL ENGDSVTSPE KVAPGEGSDL ELLSSLLPQL TGPVLELPEA 1350
TRAPLEELML EGDLLEVTLD ENHSIWQLLQ AGKPPDLARI RTLLELEKAE 1400
RHGSRARGRA LERRRRRKVD RGGEGDDPAR EELEPKRVRS SWPEAEEAHE 1450
EEELEEETGG EGPPQPLPAT GSPSTQENQN GLEPALGASS GSSVPFSTLT 1500
PRLHMSCPQQ PPQQQL 1516
Length:1,516
Mass (Da):170,584
Last modified:February 6, 2007 - v1
Checksum:i8DE6C52868E3E7E3
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
EF139241 mRNA. Translation: ABL74503.1.
RefSeqiNP_001090902.1. NM_001097433.1.
UniGeneiSsc.25162.

Genome annotation databases

GeneIDi100037295.
KEGGissc:100037295.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
EF139241 mRNA. Translation: ABL74503.1 .
RefSeqi NP_001090902.1. NM_001097433.1.
UniGenei Ssc.25162.

3D structure databases

ProteinModelPortali A1YVX4.
SMRi A1YVX4. Positions 22-147, 278-353.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 100037295.
KEGGi ssc:100037295.

Organism-specific databases

CTDi 8242.

Phylogenomic databases

eggNOGi NOG327026.
KOi K11446.

Family and domain databases

Gene3Di 1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProi IPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view ]
Pfami PF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 1 hit.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view ]
SMARTi SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view ]
SUPFAMi SSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEi PS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Yi L., Xu Y.
    Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Entry informationi

Entry nameiKDM5C_PIG
AccessioniPrimary (citable) accession number: A1YVX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: February 6, 2007
Last modified: February 19, 2014
This is version 45 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi