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A1YVX4

- KDM5C_PIG

UniProt

A1YVX4 - KDM5C_PIG

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Protein

Lysine-specific demethylase 5C

Gene

KDM5C

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).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; catalyticPROSITE-ProRule annotation
Metal bindingi476 – 4761Iron; catalyticPROSITE-ProRule annotation
Metal bindingi561 – 5611Iron; catalyticPROSITE-ProRule annotation

Regions

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

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15161516Lysine-specific demethylase 5CPRO_0000292417Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei276 – 2761PhosphoserineBy similarity
Modified residuei1318 – 13181PhosphoserineBy 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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 5542JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini24 – 128105ARIDPROSITE-ProRule annotationAdd
BLAST
Domaini427 – 593167JmjCPROSITE-ProRule annotationAdd
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

Belongs to the JARID1 histone demethylase family.Curated
Contains 1 ARID domain.PROSITE-ProRule annotation
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

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

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG327026.
InParanoidiA1YVX4.
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

« Hide

        10         20         30         40         50
MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA
60 70 80 90 100
DWQPPFAVEV DNFRFTPRIQ RLNELEIVVE EGGYEAICKD RRWARVAQRL
110 120 130 140 150
NYPPGKNIGS LLRSHYERIV YPYEMYQSGA NLVQCNTRPF DNEEKDKEYK
160 170 180 190 200
PHSIPLRQSV QPSKFNSYGR RAKRLQPDPE PTEEDIEKNP ELKKLQIYGA
210 220 230 240 250
GPKMMGLGLM AKDKTLRKKD KEGPECPPTV VVKEESGGDV KVESTSPKTF
260 270 280 290 300
LESKEELSHS PEPCTKMTMR LRRNHSNAQF IESYVCRMCS RGDEDDKLLL
310 320 330 340 350
CDGCDDNYHI FCLLPPLPEI PKGVWRCPKC VMAECKRPPE AFGFEQATRE
360 370 380 390 400
YTLQSFGEMA DSFKADYSNM PVHMVPTELV EKEFWRLVNS IEEDVTVEYG
410 420 430 440 450
ADIHSKEFGS GFPVSDSKRH LTPEEEEYAT SGWNLNVMPV LEQSVLCHIN
460 470 480 490 500
ADISGMKVPW LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA
510 520 530 540 550
AEHLEEVMKK LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG
560 570 580 590 600
EFVITFPRAY HSGFNQGYNF AEAVNFCTAD WLPAGRQCIE HYRRLRRYCV
610 620 630 640 650
FSHEELICKM AACPEKLDLN LAAAVHKEMF IMVQEERRLR KALLEKGITE
660 670 680 690 700
AEREAFELLP DDERQCIKCK TTCFLSALAC YDCPDGLVCL SHINDLCKCS
710 720 730 740 750
SSRQYLRYRY TLDELPAMLH KLKVRAESFD TWANKVRVAL EVEDGRKRSL
760 770 780 790 800
EELRALESEA RERRFPNSEL LQRLKNCLSE AEACVSRALG LVSGQEAGPH
810 820 830 840 850
RVAGLQMTLA ELRAFLDQMN NLPCAMHQIG DVKGILEQVE AYQAEAREAL
860 870 880 890 900
ASLPSSPGLL QSLLERGRQL GVEVPEAQQL QRQVEQARWL DEVKRTLAPS
910 920 930 940 950
ARRGTLAVMR GLLVAGASVA PSPAVDKAQA ELQELLTIAE RWEEKAHLCL
960 970 980 990 1000
EARQKHPPAT LEAIIHEAEN IPVHLPNIQA LKEALAKARA WIADVDEIQN
1010 1020 1030 1040 1050
GDHYPCLDDL EGLVAVGRDL PVGLEELRQL ELQVLTAHSW REKASKTFLK
1060 1070 1080 1090 1100
KNSCYTLLEV LCPCADAGSD STKRSRWMEK ELGLYKSDTE LLGLSAQDLR
1110 1120 1130 1140 1150
DPGSVIVAFK EGEQKEKEGI LQLRRTNSAK PSPLASPNTS SSATSICVCG
1160 1170 1180 1190 1200
QVPAGVGALQ CDLCQDWFHG RCVSVPRLLS SPRPSPTSSP LLAWWEWDTK
1210 1220 1230 1240 1250
FLCPLCMRSR RPRLETILAL LVALQRLPVR LPEGEALQCL TERAISWQGR
1260 1270 1280 1290 1300
ARQALAFEDV TALLGRLAEL RQRLQAEPRP EEPPTYPSTP AFDPLREGSG
1310 1320 1330 1340 1350
KDMPKVQGLL ENGDSVTSPE KVAPGEGSDL ELLSSLLPQL TGPVLELPEA
1360 1370 1380 1390 1400
TRAPLEELML EGDLLEVTLD ENHSIWQLLQ AGKPPDLARI RTLLELEKAE
1410 1420 1430 1440 1450
RHGSRARGRA LERRRRRKVD RGGEGDDPAR EELEPKRVRS SWPEAEEAHE
1460 1470 1480 1490 1500
EEELEEETGG EGPPQPLPAT GSPSTQENQN GLEPALGASS GSSVPFSTLT
1510
PRLHMSCPQQ PPQQQL
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.
InParanoidi A1YVX4.
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: October 29, 2014
This is version 47 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