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Q9BY66 (KDM5D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Lysine-specific demethylase 5D

EC=1.14.11.-
Alternative name(s):
Histocompatibility Y antigen
Short name=H-Y
Histone demethylase JARID1D
Jumonji/ARID domain-containing protein 1D
Protein SmcY
Gene names
Name:KDM5D
Synonyms:HY, HYA, JARID1D, KIAA0234, SMCY
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1539 AA.
Sequence statusComplete.
Protein existenceEvidence 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.10 Ref.11 Ref.12

Cofactor

Ascorbate. Ref.10

Binds 1 Fe2+ ion per subunit. Ref.10

Subunit structure

Interacts with PCGF6 and MSH5. Ref.10 Ref.13

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.

Sequence caution

The sequence BAA13241.2 differs from that shown. Reason: Erroneous initiation.

Alternative products

This entry describes 3 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.
Isoform 3 (identifier: Q9BY66-3)

The sequence of this isoform differs from the canonical sequence as follows:
     457-457: K → KRQSLTVLTRLISSFWAQAVLPPWPPKVLGLQ
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 15391539Lysine-specific demethylase 5D
PRO_0000200588

Regions

Domain14 – 5542JmjN
Domain79 – 16991ARID
Domain458 – 624167JmjC
Zinc finger316 – 36247PHD-type 1
Zinc finger1174 – 123562PHD-type 2

Sites

Metal binding5041Iron; catalytic By similarity
Metal binding5071Iron; catalytic By similarity
Metal binding5921Iron; catalytic By similarity

Natural variations

Alternative sequence118 – 17457Missing in isoform 2.
VSP_000317
Alternative sequence4571K → KRQSLTVLTRLISSFWAQAV LPPWPPKVLGLQ in isoform 3.
VSP_043320
Natural variant11861V → L. Ref.1
Corresponds to variant rs1050807 [ dbSNP | Ensembl ].
VAR_032991

Experimental info

Mutagenesis5341H → A: Abolishes enzymatic activity; when associated with A-536. Ref.10
Mutagenesis5361E → A: Abolishes enzymatic activity; when associated with A-534. Ref.10
Sequence conflict3271D → N in AAC50806. Ref.1
Sequence conflict3271D → N in AAC51135. Ref.8
Sequence conflict12851S → F in AAC50806. Ref.1
Sequence conflict13521P → L in AAK27839. Ref.9
Sequence conflict13911D → G in AAC50806. Ref.1

Secondary structure

......................... 1539
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 24, 2001. Version 2.
Checksum: E58DAE374E3BD7AA

FASTA1,539174,073
        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 

« Hide

Isoform 2 [UniParc].

Checksum: F1A41999427CA63D
Show »

FASTA1,482167,401
Isoform 3 [UniParc].

Checksum: 364A4C31873A1D57
Show »

FASTA1,570177,558

References

« Hide '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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
[5]"The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes."
Skaletsky H., Kuroda-Kawaguchi T., Minx P.J., Cordum H.S., Hillier L.W., Brown L.G., Repping S., Pyntikova T., Ali J., Bieri T., Chinwalla A., Delehaunty A., Delehaunty K., Du H., Fewell G., Fulton L., Fulton R., Graves T.A. expand/collapse author list , Hou S.-F., Latrielle P., Leonard S., Mardis E., Maupin R., McPherson J., Miner T., Nash W., Nguyen C., Ozersky P., Pepin K., Rock S., Rohlfing T., Scott K., Schultz B., Strong C., Tin-Wollam A., Yang S.-P., Waterston R.H., Wilson R.K., Rozen S., Page D.C.
Nature 423:825-837(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]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. expand/collapse author list , 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].
[7]"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] (ISOFORMS 1; 2 AND 3).
[8]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-457 (ISOFORM 1).
[9]"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.
[10]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR, INTERACTION WITH PCGF6, MUTAGENESIS OF HIS-534 AND GLU-536.
[11]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[12]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[13]"Spermatogenesis-specific association of SMCY and MSH5."
Akimoto C., Kitagawa H., Matsumoto T., Kato S.
Genes Cells 13:623-633(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH MSH5.
[14]"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

EMBL
GenBank
DDBJ
U52191 mRNA. Translation: AAC50806.1.
D87072 mRNA. Translation: BAA13241.2. Different initiation.
AF273841 Genomic DNA. Translation: AAG00951.1.
AC010889 Genomic DNA. No translation available.
CH471202 Genomic DNA. Translation: EAW54663.1.
BC132721 mRNA. Translation: AAI32722.1.
BC144102 mRNA. Translation: AAI44103.1.
BC146767 mRNA. Translation: AAI46768.1.
U52365 mRNA. Translation: AAC51135.1.
AF134849 Genomic DNA. Translation: AAK27839.1.
CCDSCCDS14794.1. [Q9BY66-1]
CCDS55554.1. [Q9BY66-2]
CCDS55555.1. [Q9BY66-3]
RefSeqNP_001140177.1. NM_001146705.1. [Q9BY66-3]
NP_001140178.1. NM_001146706.1. [Q9BY66-2]
NP_004644.2. NM_004653.4. [Q9BY66-1]
UniGeneHs.80358.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2E6RNMR-A306-384[»]
2YQENMR-A79-171[»]
ProteinModelPortalQ9BY66.
SMRQ9BY66. Positions 13-76, 79-171, 309-606, 1173-1240.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113891. 3 interactions.
IntActQ9BY66. 1 interaction.
STRING9606.ENSP00000322408.

Chemistry

DrugBankDB00126. Vitamin C.

PTM databases

PhosphoSiteQ9BY66.

Polymorphism databases

DMDM17368706.

Proteomic databases

MaxQBQ9BY66.
PaxDbQ9BY66.
PRIDEQ9BY66.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000317961; ENSP00000322408; ENSG00000012817. [Q9BY66-1]
ENST00000382806; ENSP00000372256; ENSG00000012817. [Q9BY66-2]
ENST00000541639; ENSP00000444293; ENSG00000012817. [Q9BY66-3]
GeneID8284.
KEGGhsa:8284.
UCSCuc004fug.3. human. [Q9BY66-1]
uc010nwy.3. human. [Q9BY66-2]
uc011naz.2. human. [Q9BY66-3]

Organism-specific databases

CTD8284.
GeneCardsGC0YM021865.
GeneReviewsKDM5D.
HGNCHGNC:11115. KDM5D.
HPAHPA049086.
MIM426000. gene.
neXtProtNX_Q9BY66.
PharmGKBPA35965.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG327026.
HOGENOMHOG000290719.
InParanoidQ9BY66.
KOK11446.
OMAGREEEHY.
OrthoDBEOG7D85VK.
PhylomeDBQ9BY66.
TreeFamTF106476.

Gene expression databases

ArrayExpressQ9BY66.
BgeeQ9BY66.
CleanExHS_JARID1D.
GenevestigatorQ9BY66.

Family and domain databases

Gene3D1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProIPR001606. 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]
PfamPF01388. 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]
SMARTSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]
SUPFAMSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEPS51011. 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]
ProtoNetSearch...

Other

ChiTaRSKDM5D. human.
EvolutionaryTraceQ9BY66.
GeneWikiJARID1D.
GenomeRNAi8284.
NextBio31049.
PROQ9BY66.
SOURCESearch...

Entry information

Entry nameKDM5D_HUMAN
AccessionPrimary (citable) accession number: Q9BY66
Secondary accession number(s): A2RU19 expand/collapse secondary AC list , A6H8V7, B7ZLX1, Q92509, Q92809, Q9HCU1
Entry history
Integrated into UniProtKB/Swiss-Prot: October 24, 2001
Last sequence update: October 24, 2001
Last modified: July 9, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome Y

Human chromosome Y: entries, gene names and cross-references to MIM