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UniProtKB/Swiss-Prot entry O94953


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name KDM4B_HUMAN
Primary accession number O94953
Secondary accession numbers O75274 Q6P3R5 Q9P1V1 Q9UF40
Integrated into Swiss-Prot on February 16, 2004
Sequence was last modified on March 20, 2007 (Sequence version 4)
Annotations were last modified on    June 16, 2009 (Entry version 73)
Name and origin of the protein
Protein name Lysine-specific demethylase 4B
Synonyms EC 1.14.11.-
JmjC domain-containing histone demethylation protein 3B
Jumonji domain-containing protein 2B
Gene name
Name: KDM4B
Synonyms: JHDM3B, JMJD2B, KIAA0876
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT GLU-710.
TISSUE=Brain;
DOI=10.1093/dnares/5.6.355; PubMed=10048485 [NCBI, ExPASy, EBI, Israel, Japan]
Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.;
"Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.";
DNA Res. 5:355-364(1998).
[2]
SEQUENCE REVISION.
DOI=10.1093/dnares/9.3.99; PubMed=12168954 [NCBI, ExPASy, EBI, Israel, Japan]
Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.;
"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones.";
DNA Res. 9:99-106(2002).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1038/nature02399; PubMed=15057824 [NCBI, ExPASy, EBI, Israel, Japan]
Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V., Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.;
"The DNA sequence and biology of human chromosome 19.";
Nature 428:529-535(2004).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), AND VARIANT GLU-710.
TISSUE=Testis;
DOI=10.1101/gr.2596504; PubMed=15489334 [NCBI, ExPASy, EBI, Israel, Japan]
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 487-1096, AND VARIANT GLU-710.
TISSUE=Testis;
DOI=10.1186/1471-2164-8-399; PubMed=17974005 [NCBI, ExPASy, EBI, Israel, Japan]
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Blocker H., Heubner D., Hoerlein A., Michel G., Wedler H., Kohrer K., Ottenwalder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[6]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-566 AND SER-622, AND MASS SPECTROMETRY.
TISSUE=Epithelium;
DOI=10.1073/pnas.0404720101; PubMed=15302935 [NCBI, ExPASy, EBI, Israel, Japan]
Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P.;
"Large-scale characterization of HeLa cell nuclear phosphoproteins.";
Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004).
[7]
SUBCELLULAR LOCATION.
DOI=10.1074/jbc.M413687200; PubMed=15927959 [NCBI, ExPASy, EBI, Israel, Japan]
Gray S.G., Iglesias A.H., Lizcano F., Villanueva R., Camelo S., Jingu H., Teh B.T., Koibuchi N., Chin W.W., Kokkotou E., Dangond F.;
"Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein.";
J. Biol. Chem. 280:28507-28518(2005).
[8]
FUNCTION, AND ENZYME ACTIVITY.
DOI=10.1016/j.cell.2006.03.028; PubMed=16603238 [NCBI, ExPASy, EBI, Israel, Japan]
Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y.;
"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases.";
Cell 125:467-481(2006).
Comments
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AB020683; BAA74899.2; ALT_INIT; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AC005595; AAC33799.1; ALT_SEQ; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AC022517; AAF31271.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC063889; AAH63889.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL133622; CAB63748.2; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
IPI IPI00013205; -.
IPI00440491; -.
PIR T43460; T43460.
RefSeq NP_055830.1; -.
UniGene Hs.654816
3D structure databases
SMR O94953; 10-348.
ModBase O94953.
Protein-protein interaction databases
IntAct O94953; 1.
PTM databases
PhosphoSite O94953; -.
Organism-specific databases
GeneCards GC19P004920; -.
H-InvDB HIX0018637; -.
HGNC HGNC:29136; KDM4B.
GenAtlas KDM4B.
MIM 609765; gene. [NCBI / EBI]
PharmGKB PA134885213; -.
HUGE KIAA0876.
Gene expression databases
ArrayExpress O94953; -.
Bgee O94953; -.
CleanEx HS_JMJD2B; -.
Ontologies
GO
GO:0005634; Cellular component: nucleus (inferred from electronic annotation from UniProtKB-SubCell).
GO:0005506; Molecular function: iron ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0003676; Molecular function: nucleic acid binding (inferred from electronic annotation from InterPro).
GO:0016702; Molecular function: oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (inferred from electronic annotation from UniProtKB-KW).
GO:0005515; Molecular function: protein binding (inferred from electronic annotation from InterPro).
GO:0008270; Molecular function: zinc ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0016568; Biological process: chromatin modification (inferred from electronic annotation from UniProtKB-KW).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
GO:0006355; Biological process: regulation of transcription, DNA-dependent (inferred from electronic annotation from UniProtKB-KW).
GO:0006350; Biological process: transcription (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR019023; Lamin-B_rcpt_of_tudor.
IPR013129; TF_JmjC.
IPR003347; TF_JmjC_AAH.
IPR003349; TF_JmjN.
IPR002999; Tudor.
IPR019786; Zinc_finger_PHD-type_CS.
IPR001965; Znf_PHD.
IPR019787; Znf_PHD-finger.
Graphical view of domain structure.
Pfam PF02373; JmjC; 1.
PF02375; JmjN; 1.
PF09465; LBR_tudor; 1.
PF00628; PHD; 1.
Pfam graphical view of domain structure.
SMART SM00558; JmjC; 1.
SM00545; JmjN; 1.
SM00249; PHD; 2.
SM00333; TUDOR; 2.
SMART graphical view of domain structure.
PROSITE PS51184; JMJC; 1.
PS51183; JMJN; 1.
PS50304; TUDOR; FALSE_NEG.
PS01359; ZF_PHD_1; FALSE_NEG.
PS50016; ZF_PHD_2; FALSE_NEG.
PROSITE graphical view of domain structure (profiles).
Proteomic databases
PRIDE O94953; -.
Genome annotation databases
Ensembl ENSG00000127663; Homo sapiens. [Contig view]
GeneID 23030; -.
KEGG hsa:23030; -.
NMPDR fig|9606.3.peg.15454; -.
Phylogenomic databases
HOGENOM O94953; -.
HOVERGEN O94953; -.
OMA O94953; GDTEAGP.
Other
SOURCE KDM4B; Homo sapiens.
ProtoNet O94953.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Alternative splicing; Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; Polymorphism; Repeat; Transcription; Transcription regulation; Zinc; Zinc-finger.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   1096  1096     Lysine-specific demethylase 4B. PRO_0000183175
DOMAIN   15     57  43     JmjN. 
DOMAIN   146    309  164     JmjC. 
DOMAIN   917    974  58     Tudor 1. 
DOMAIN   975   1031  57     Tudor 2. 
ZN_FING   731    789  59     PHD-type 1. 
ZN_FING   851    907  57     PHD-type 2. 
COMPBIAS   463    535  73     Pro-rich. 
METAL   189    189        Iron; catalytic (By similarity). 
METAL   191    191        Iron; catalytic (By similarity). 
METAL   235    235        Zinc (By similarity). 
METAL   241    241        Zinc (By similarity). 
METAL   277    277        Iron; catalytic (By similarity). 
METAL   307    307        Zinc (By similarity). 
METAL   309    309        Zinc (By similarity). 
BINDING   133    133        Alpha-ketoglutarate (By similarity). 
BINDING   199    199        Alpha-ketoglutarate (By similarity). 
BINDING   207    207        Alpha-ketoglutarate (By similarity). 
MOD_RES   305    305        Phosphothreonine (By similarity). 
MOD_RES   566    566        Phosphoserine. 
MOD_RES   622    622        Phosphoserine. 
VAR_SEQ   373    448        SHRKRSQPKKPKPEDPKFPGEGTAGAALLEEAGGSVKEEA GPEVDPEEEEEEPQPLPHGREAEGAEEDGRGKLRPT -> TPPCVSPHRPSQPGIWCPPGGEAKASAASWLLTTRGHGDT EAGPGLGGDPLHAQSEGQASCVSTSRLRMATQDPCR (in isoform 2). VSP_018307
VAR_SEQ   449   1096        Missing (in isoform 2). VSP_018308
VARIANT   29     29  1     N -> T (in dbSNP:rs11667206 [NCBI]). VAR_026223 [3D]
VARIANT   710    710  1     K -> E (in dbSNP:rs2620836 [NCBI]). VAR_026224 
Sequence information
Length: 1096 AA [This is the length of the unprocessed precursor] Molecular weight: 121897 Da [This is the MW of the unprocessed precursor] CRC64: 300D5CD6F2DD4330 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MGSEDHGAQN PSCKIMTFRP TMEEFKDFNK YVAYIESQGA HRAGLAKIIP PKEWKPRQTY 

        70         80         90        100        110        120 
DDIDDVVIPA PIQQVVTGQS GLFTQYNIQK KAMTVGEYRR LANSEKYCTP RHQDFDDLER 

       130        140        150        160        170        180 
KYWKNLTFVS PIYGADISGS LYDDDVAQWN IGSLRTILDM VERECGTIIE GVNTPYLYFG 

       190        200        210        220        230        240 
MWKTTFAWHT EDMDLYSINY LHFGEPKSWY AIPPEHGKRL ERLAIGFFPG SSQGCDAFLR 

       250        260        270        280        290        300 
HKMTLISPII LKKYGIPFSR ITQEAGEFMI TFPYGYHAGF NHGFNCAEST NFATLRWIDY 

       310        320        330        340        350        360 
GKVATQCTCR KDMVKISMDV FVRILQPERY ELWKQGKDLT VLDHTRPTAL TSPELSSWSA 

       370        380        390        400        410        420 
SRASLKAKLL RRSHRKRSQP KKPKPEDPKF PGEGTAGAAL LEEAGGSVKE EAGPEVDPEE 

       430        440        450        460        470        480 
EEEEPQPLPH GREAEGAEED GRGKLRPTKA KSERKKKSFG LLPPQLPPPP AHFPSEEALW 

       490        500        510        520        530        540 
LPSPLEPPVL GPGPAAMEES PLPAPLNVVP PEVPSEELEA KPRPIIPMLY VVPRPGKAAF 

       550        560        570        580        590        600 
NQEHVSCQQA FEHFAQKGPT WKEPVSPMEL TGPEDGAASS GAGRMETKAR AGEGQAPSTF 

       610        620        630        640        650        660 
SKLKMEIKKS RRHPLGRPPT RSPLSVVKQE ASSDEEASPF SGEEDVSDPD ALRPLLSLQW 

       670        680        690        700        710        720 
KNRAASFQAE RKFNAAAART EPYCAICTLF YPYCQALQTE KEAPIASLGK GCPATLPSKS 

       730        740        750        760        770        780 
RQKTRPLIPE MCFTSGGENT EPLPANSYIG DDGTSPLIAC GKCCLQVHAS CYGIRPELVN 

       790        800        810        820        830        840 
EGWTCSRCAA HAWTAECCLC NLRGGALQMT TDRRWIHVIC AIAVPEARFL NVIERHPVDI 

       850        860        870        880        890        900 
SAIPEQRWKL KCVYCRKRMK KVSGACIQCS YEHCSTSFHV TCAHAAGVLM EPDDWPYVVS 

       910        920        930        940        950        960 
ITCLKHKSGG HAVQLLRAVS LGQVVITKNR NGLYYRCRVI GAASQTCYEV NFDDGSYSDN 

       970        980        990       1000       1010       1020 
LYPESITSRD CVQLGPPSEG ELVELRWTDG NLYKAKFISS VTSHIYQVEF EDGSQLTVKR 

      1030       1040       1050       1060       1070       1080 
GDIFTLEEEL PKRVRSRLSL STGAPQEPAF SGEEAKAAKR PRVGTPLATE DSGRSQDYVA 

      1090 
FVESLLQVQG RPGAPF 

O94953 in FASTA format

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