Reviewed, UniProtKB/Swiss-Prot Q9BY66 (KDM5D_HUMAN)

Names and origin

Protein names

Recommended name:
    Lysine-specific demethylase 5D
    EC=1.14.11.-
Alternative name(s):
    Histone demethylase JARID1D
    Jumonji/ARID domain-containing protein 1D
    Protein SmcY
    Histocompatibility Y antigen
      Short name=H-Y

Gene names

Name:	KDM5D
Synonyms:	HY, HYA, JARID1D, KIAA0234, SMCY

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1539 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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'. May play a role in spermatogenesis. Ref.9 Ref.10 Ref.11
Cofactor	Ascorbate. Ref.9 Fe2+. Ref.9
Subunit structure	Interacts with PCGF6. Ref.9
Subcellular location	Nucleus Probable.
Domain	The JmjC domain is required for enzymatic activity.
Sequence similarities	Belongs to the JARID1 histone demethylase family. Contains 1 ARID domain. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 2 PHD-type zinc fingers.

Ontologies

Keywords
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Zinc-finger
Ligand	Iron Metal-binding Zinc
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW spermatogenesis Non-traceable author statement. Source: UniProtKB
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW protein binding Ref.10 Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P68432	1	EBI-1246860,EBI-79764	From a different organism.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.

Isoform 1 (identifier: Q9BY66-1)

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.

Isoform 2 (identifier: Q9BY66-2)

The sequence of this isoform differs from the canonical sequence as follows:
     118-174: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1539

1539

Lysine-specific demethylase 5D

PRO_0000200588

Regions

Domain

14 – 55

42

JmjN

Domain

79 – 169

91

ARID

Domain

458 – 624

167

JmjC

Zinc finger

316 – 362

47

PHD-type 1

Zinc finger

1174 – 1235

62

PHD-type 2

Natural variations

Alternative sequence

118 – 174

57

Missing in isoform 2.

VSP_000317

Natural variant

1186

1

V → L: dbSNP rs1050807. Ref.1

VAR_032991

Experimental info

Mutagenesis

534

1

H → A: Abolishes enzymatic activity; when associated with A-536. Ref.9

Mutagenesis

536

1

E → A: Abolishes enzymatic activity; when associated with A-534. Ref.9

Sequence conflict

327

1

D → N in AAC50806. Ref.1

Sequence conflict

327

1

D → N in AAC51135. Ref.7

Sequence conflict

1285

1

S → F in AAC50806. Ref.1

Sequence conflict

1352

1

P → L in AAK27839. Ref.8

Sequence conflict

1391

1

D → G in AAC50806. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

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.

.

.

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.

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1539

Helix Strand Turn

Details...

Helix

81 – 96

16

Beta strand

106 – 109

4

Helix

112 – 122

11

Helix

125 – 130

6

Turn

131 – 133

3

Helix

134 – 140

7

Helix

149 – 159

11

Helix

161 – 167

7

Beta strand

318 – 320

3

Helix

324 – 328

5

Turn

333 – 335

3

Beta strand

341 – 346

6

Helix

359 – 366

8

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 24, 2001. Version 2. Checksum: E58DAE374E3BD7AA	FASTA	1,539	174,073
	10 20 30 40 50 60 MEPGCDEFLP PPECPVFEPS WAEFQDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 70 80 90 100 110 120 DNFRFTPRVQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLSKIVI 130 140 150 160 170 180 EEGGYEAICK DRRWARVAQR LHYPPGKNIG SLLRSHYERI IYPYEMFQSG ANHVQCNTHP 190 200 210 220 230 240 FDNEVKDKEY KPHSIPLRQS VQPSKFSSYS RRAKRLQPDP EPTEEDIEKH PELKKLQIYG 250 260 270 280 290 300 PGPKMMGLGL MAKDKDKTVH KKVTCPPTVT VKDEQSGGGN VSSTLLKQHL SLEPCTKTTM 310 320 330 340 350 360 QLRKNHSSAQ FIDSYICQVC SRGDEDDKLL FCDGCDDNYH IFCLLPPLPE IPRGIWRCPK 370 380 390 400 410 420 CILAECKQPP EAFGFEQATQ EYSLQSFGEM ADSFKSDYFN MPVHMVPTEL VEKEFWRLVS 430 440 450 460 470 480 SIEEDVTVEY GADIHSKEFG SGFPVSNSKQ NLSPEEKEYA TSGWNLNVMP VLDQSVLCHI 490 500 510 520 530 540 NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL AAEHLEEVMK 550 560 570 580 590 600 MLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA YHSGFNQGYN 610 620 630 640 650 660 FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAAFPETLDL NLAVAVHKEM 670 680 690 700 710 720 FIMVQEERRL RKALLEKGVT EAEREAFELL PDDERQCIKC KTTCFLSALA CYDCPDGLVC 730 740 750 760 770 780 LSHINDLCKC SSSRQYLRYR YTLDELPTML HKLKIRAESF DTWANKVRVA LEVEDGRKRS 790 800 810 820 830 840 FEELRALESE ARERRFPNSE LLQRLKNCLS EVEACIAQVL GLVSGQVARM DTPQLTLTEL 850 860 870 880 890 900 RVLLEQMGSL PCAMHQIGDV KDVLEQVEAY QAEAREALAT LPSSPGLLRS LLERGQQLGV 910 920 930 940 950 960 EVPEAHQLQQ QVEQAQWLDE VKQALAPSAH RGSLVIMQGL LVMGAKIASS PSVDKARAEL 970 980 990 1000 1010 1020 QELLTIAERW EEKAHFCLEA RQKHPPATLE AIIRETENIP VHLPNIQALK EALTKAQAWI 1030 1040 1050 1060 1070 1080 ADVDEIQNGD HYPCLDDLEG LVAVGRDLPV GLEELRQLEL QVLTAHSWRE KASKTFLKKN 1090 1100 1110 1120 1130 1140 SCYTLLEVLC PCADAGSDST KRSRWMEKAL GLYQCDTELL GLSAQDLRDP GSVIVAFKEG 1150 1160 1170 1180 1190 1200 EQKEKEGILQ LRRTNSAKPS PLAPSLMASS PTSICVCGQV PAGVGVLQCD LCQDWFHGQC 1210 1220 1230 1240 1250 1260 VSVPHLLTSP KPSLTSSPLL AWWEWDTKFL CPLCMRSRRP RLETILALLV ALQRLPVRLP 1270 1280 1290 1300 1310 1320 EGEALQCLTE RAIGWQDRAR KALASEDVTA LLRQLAELRQ QLQAKPRPEE ASVYTSATAC 1330 1340 1350 1360 1370 1380 DPIREGSGNN ISKVQGLLEN GDSVTSPENM APGKGSDLEL LSSLLPQLTG PVLELPEAIR 1390 1400 1410 1420 1430 1440 APLEELMMEG DLLEVTLDEN HSIWQLLQAG QPPDLDRIRT LLELEKFEHQ GSRTRSRALE 1450 1460 1470 1480 1490 1500 RRRRRQKVDQ GRNVENLVQQ ELQSKRARSS GIMSQVGREE EHYQEKADRE NMFLTPSTDH 1510 1520 1530 SPFLKGNQNS LQHKDSGSSA ACPSLMPLLQ LSYSDEQQL
	Isoform 2. Checksum: F1A41999427CA63D	FASTA	1,482	167,401
	10 20 30 40 50 60 MEPGCDEFLP PPECPVFEPS WAEFQDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 70 80 90 100 110 120 DNFRFTPRVQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLSKQCN 130 140 150 160 170 180 THPFDNEVKD KEYKPHSIPL RQSVQPSKFS SYSRRAKRLQ PDPEPTEEDI EKHPELKKLQ 190 200 210 220 230 240 IYGPGPKMMG LGLMAKDKDK TVHKKVTCPP TVTVKDEQSG GGNVSSTLLK QHLSLEPCTK 250 260 270 280 290 300 TTMQLRKNHS SAQFIDSYIC QVCSRGDEDD KLLFCDGCDD NYHIFCLLPP LPEIPRGIWR 310 320 330 340 350 360 CPKCILAECK QPPEAFGFEQ ATQEYSLQSF GEMADSFKSD YFNMPVHMVP TELVEKEFWR 370 380 390 400 410 420 LVSSIEEDVT VEYGADIHSK EFGSGFPVSN SKQNLSPEEK EYATSGWNLN VMPVLDQSVL 430 440 450 460 470 480 CHINADISGM KVPWLYVGMV FSAFCWHIED HWSYSINYLH WGEPKTWYGV PSLAAEHLEE 490 500 510 520 530 540 VMKMLTPELF DSQPDLLHQL VTLMNPNTLM SHGVPVVRTN QCAGEFVITF PRAYHSGFNQ 550 560 570 580 590 600 GYNFAEAVNF CTADWLPAGR QCIEHYRRLR RYCVFSHEEL ICKMAAFPET LDLNLAVAVH 610 620 630 640 650 660 KEMFIMVQEE RRLRKALLEK GVTEAEREAF ELLPDDERQC IKCKTTCFLS ALACYDCPDG 670 680 690 700 710 720 LVCLSHINDL CKCSSSRQYL RYRYTLDELP TMLHKLKIRA ESFDTWANKV RVALEVEDGR 730 740 750 760 770 780 KRSFEELRAL ESEARERRFP NSELLQRLKN CLSEVEACIA QVLGLVSGQV ARMDTPQLTL 790 800 810 820 830 840 TELRVLLEQM GSLPCAMHQI GDVKDVLEQV EAYQAEAREA LATLPSSPGL LRSLLERGQQ 850 860 870 880 890 900 LGVEVPEAHQ LQQQVEQAQW LDEVKQALAP SAHRGSLVIM QGLLVMGAKI ASSPSVDKAR 910 920 930 940 950 960 AELQELLTIA ERWEEKAHFC LEARQKHPPA TLEAIIRETE NIPVHLPNIQ ALKEALTKAQ 970 980 990 1000 1010 1020 AWIADVDEIQ NGDHYPCLDD LEGLVAVGRD LPVGLEELRQ LELQVLTAHS WREKASKTFL 1030 1040 1050 1060 1070 1080 KKNSCYTLLE VLCPCADAGS DSTKRSRWME KALGLYQCDT ELLGLSAQDL RDPGSVIVAF 1090 1100 1110 1120 1130 1140 KEGEQKEKEG ILQLRRTNSA KPSPLAPSLM ASSPTSICVC GQVPAGVGVL QCDLCQDWFH 1150 1160 1170 1180 1190 1200 GQCVSVPHLL TSPKPSLTSS PLLAWWEWDT KFLCPLCMRS RRPRLETILA LLVALQRLPV 1210 1220 1230 1240 1250 1260 RLPEGEALQC LTERAIGWQD RARKALASED VTALLRQLAE LRQQLQAKPR PEEASVYTSA 1270 1280 1290 1300 1310 1320 TACDPIREGS GNNISKVQGL LENGDSVTSP ENMAPGKGSD LELLSSLLPQ LTGPVLELPE 1330 1340 1350 1360 1370 1380 AIRAPLEELM MEGDLLEVTL DENHSIWQLL QAGQPPDLDR IRTLLELEKF EHQGSRTRSR 1390 1400 1410 1420 1430 1440 ALERRRRRQK VDQGRNVENL VQQELQSKRA RSSGIMSQVG REEEHYQEKA DRENMFLTPS 1450 1460 1470 1480 TDHSPFLKGN QNSLQHKDSG SSAACPSLMP LLQLSYSDEQ QL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Gene sequence and evolutionary conservation of human SMCY." Kent-First M.G., Maffitt M., Muallem A., Brisco P., Shultz J., Ekenberg S., Agulnik A.I., Agulnik S.I., Shramm D., Bavister B., Abdul-Mawgood A., Vandeberg J. Nat. Genet. 14:128-129(1996) [PubMed: 8841177] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT LEU-1186.
[2]	Erratum Kent-First M.G., Maffitt M., Muallem A., Brisco P., Shultz J., Ekenberg S., Agulnik A.I., Agulnik S.I., Shramm D., Bavister B., Abdul-Mawgood A., Vandeberg J. Nat. Genet. 14:252-252(1996)
[3]	"Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain." Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N. DNA Res. 3:321-329(1996) [PubMed: 9039502] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Bone marrow.
[4]	"Population genetic implications from sequence variation in four Y chromosome genes." Shen P., Wang F., Underhill P.A., Franco C., Yang W.-H., Roxas A., Sung R., Lin A.A., Hyman R.W., Vollrath D., Davis R.W., Cavalli-Sforza L.L., Oefner P.J. Proc. Natl. Acad. Sci. U.S.A. 97:7354-7359(2000) [PubMed: 10861003] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases 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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
[7]	"Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven." Agulnik A.I., Bishop C.E., Lerner J.L., Agulnik S.I., Solovyev V.V. Mamm. Genome 8:134-138(1997) [PubMed: 9060413] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-457 (ISOFORM 1).
[8]	"Exon-intron structure of SMCX and SMCY genes in bovine and swine." Poloumienko A., Blecher S. Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1340-1478. Tissue: Blood.
[9]	"Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein." Lee M.G., Norman J., Shilatifard A., Shiekhattar R. Cell 128:877-887(2007) [PubMed: 17320162] [Abstract] Cited for: FUNCTION, COFACTOR, INTERACTION WITH PCGF6, MUTAGENESIS OF HIS-534 AND GLU-536.
[10]	"The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases." Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y. Cell 128:1077-1088(2007) [PubMed: 17320160] [Abstract] Cited for: FUNCTION.
[11]	"The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase." Eissenberg J.C., Lee M.G., Schneider J., Ilvarsonn A., Shiekhattar R., Shilatifard A. Nat. Struct. Mol. Biol. 14:344-346(2007) [PubMed: 17351630] [Abstract] Cited for: FUNCTION.
[12]	"Solution structure of the PHD domain and of the ARID domain of JARID1D/SMCY protein." RIKEN structural genomics initiative (RSGI) Submitted (APR-2008) to the PDB data bank Cited for: STRUCTURE BY NMR OF 79-384.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U52191 mRNA. Translation: AAC50806.1.
D87072 mRNA. Translation: BAA13241.2. Different initiation.
AF273841 Genomic DNA. Translation: AAG00951.1.
CH471202 Genomic DNA. Translation: EAW54663.1.
BC132721 mRNA. Translation: AAI32722.1.
BC146767 mRNA. Translation: AAI46768.1.
U52365 mRNA. Translation: AAC51135.1.
AF134849 Genomic DNA. Translation: AAK27839.1.

IPI

IPI00219940.
IPI00329577.

RefSeq

NP_001140178.1.
NP_004644.2.

UniGene

Hs.80358

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2E6R	NMR	-	A	306-384	[»]
2YQE	NMR	-	A	79-171	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9BY66. 1 interaction.

STRING

Q9BY66.

PTM databases

PhosphoSite

Q9BY66.

Proteomic databases

PRIDE

Q9BY66.

Genome annotation databases

Ensembl

ENST00000317961; ENSP00000322408; ENSG00000012817; Homo sapiens. [Genome view]

GeneID

8284.

UCSC

uc004fug.1. human.
uc010nwy.1. human.

Organism-specific databases

CTD

8284.

GeneCards

GC0YM020255.

H-InvDB

HIX0017195.

HGNC

HGNC:11115. KDM5D.

MIM

426000. gene.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q9BY66.

HOVERGEN

Q9BY66.

OMA

AMKSAAP

Gene expression databases

ArrayExpress

Q9BY66.

Bgee

Q9BY66.

CleanEx

HS_JARID1D.

Genevestigator

Q9BY66.

GermOnline

ENSG00000012817. Homo sapiens.

Family and domain databases

InterPro

IPR001606. ARID.
IPR013637. PLU-1.
IPR013129. TF_JmjC.
IPR003347. TF_JmjC_AAH.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
[Graphical view]

Gene3D

G3DSA:1.10.150.60. ARID. 1 hit.

Pfam

PF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 2 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]

SMART

SM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]

PROSITE

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]

ProtoNet

Search...

Other Resources

DrugBank

DB00126. Vitamin C.

NextBio

31049.

SOURCE

Search...

Entry information

Entry name

KDM5D_HUMAN

Accession

Primary (citable) accession number: Q9BY66
Secondary accession number(s): A2RU19 , A6H8V7, Q92509, Q92809, Q9HCU1

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 24, 2001
Last sequence update:	October 24, 2001
Last modified:	November 24, 2009
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.