| General information | | DisProt: | DP00711 | | Name: | Lysine-specific demethylase 5B | | Synonym(s): | KDM5B_MOUSE
Histone demethylase JARID1B
Jumonji/ARID domain-containing protein 1B
PLU-1
| | First appeared in release: | Release 6.00 (07/01/2012) | | UniProt: | Q80Y84 | | UniGene: | | | SwissProt: | KDM5B_MOUSE | | TrEMBL: | | | NCBI (GI): | | | Source organism: | Mus musculus (Mouse) | | Sequence length: | 1544 | | Percent disordered: | 3% | | Homologues: | |
| Native sequence |
10 20 30 40 50 60
| | | | | |
MEPATTLPPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH KIRPIAEQTG - 60
ICKVRPPPDW QPPFACDVDK LHFTPRIQRL NELEAQTRVK LNFLDQIAKY WELQGSTLKI - 120
PHVERKILDL FQLNKLVAEE GGFAVVCKDR KWTKIATKMG FAPGKAVGSH IRGHYERILN - 180
PYNLFLSGDS LRCLQKPNLT SDTKDKEYKP HDIPQRQSVQ PAETCPPARR AKRMRAEAMN - 240
IKIEPEEATE ARTHNLRRRM GCTTPKWENE KEMKSTIKQE PTEKKDCELE SEKEKPKSRA - 300
KKTATAVDLY VCLLCGSGND EDRLLLCDGC DDSYHTFCLV PPLHDVPKGD WRCPKCLAQE - 360
CNKPQEAFGF EQAARDYTLR TFGEMADAFK SDYFNMPVHM VPTELVEKEF WRLVSTIEED - 420
VTVEYGADIA SKEFGSGFPV RDGKIKISPE EEEYLDSGWN LNNMPVMEQS VLAHITADIC - 480
GMKLPWLYVG MCFSSFCWHI EDHWSYSINY LHWGEPKTWY GVPGYAAEQL ENVMKKLAPE - 540
LFVSQPDLLH QLVTIMNPNT LMTHEVPVYR TNQCAGEFVI TFPRAYHSGF NQGFNFAEAV - 600
NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST VQKDMAIMIE - 660
DEKALRETVR KLGVIDSERM DFELLPDDER QCIKCKTTCF MSAISCSCKP GLLVCLHHVK - 720
ELCSCPPYKY NLRYRYTLDD LYPMMNALKL RAESYNEWAL NVNEALEAKI NKKKSLVSFK - 780
ALIEESEMKK FPDNDLLRHL RLVTQDAEKC ASVAQQLLNG KRQTRYRSGG GKSQNQLTVN - 840
ELRQFVTQLY ALPCVLSQTP LLKDLLNRVE DFQQQSQKLL SEEMPSAAEL QELLDVSFEF - 900
DVELPQLTEM RIRLEQARWL EEVQQACLDS SSLSLDDMRR LIDLGVGLAP YSAVEKAMAR - 960
LQELLTVSEH WDDKAKSLLR ARPRHSLSSL ATAVKEMEEI PAYLPNGTVL KDSVQRARDW - 1020
VQDVDALQAG GRVPVLETLI ELVARGRSIP VHLNSLPRLE MLVAEVHAWK ECAAKTFLPE - 1080
NSTYSLLEVL CPRCDIGLLG LKRKQRKLKE PLPSGKKRST KLESLSDLER ALMESKETAA - 1140
AMATLGEARL REMEALQSLR FANEEKLLSP VQDLEMKVCL CQKTPATPMI QCELCRDAFH - 1200
TSCVAAPSIS QSSRIWLCPH CRRSEKPPLE KILPLLASLQ RIRVRLPEGD ALRYMIERTV - 1260
NWQHRAQQLL SSGNLKLVQD QVGSGLLSSR WPASAGQASA TDKVSQPPGT TSFSLPDDWD - 1320
NRTSYLHSPF STGQSCLPLH GLSPEVNELL MEAQLLQVSL PEIQELYQTL LTKPSSVQQA - 1380
DRSSPVRSSS EKNDCLRGKR DAINSPERKL KRRPEREGLP SERWDRVKHM RTPQKKKIKL - 1440
SHPKDMDSFK LERERSYDLV RNAETHSLPS DTSYSEQEDS EDEDAICPAV SCLQPEGDEV - 1500
DWVQCDGSCN QWFHQVCVGV SPEMAEKEDY ICVRCTGKDA PSRK
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| Functional narrative |
Function: Histone demethylase that demethylates \'Lys-4\' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 \'Lys-9\' or H3 \'Lys-27\'. Demethylates trimethylated, dimethylated and monomethylated H3 \'Lys-4\'. Acts as a transcriptional corepressor for FOXG1B and PAX9.
COFACTOR: Binds 1 Fe(2+) ion per subunit (By similarity).
SUBUNIT: Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7 (By similarity). P68432:- (xeno); NbExp=1; IntAct=EBI-1249551, EBI-79764;
Subcellular Location: Nucleus. Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q80Y84-1; Sequence=Displayed; Name=2; IsoId=Q80Y84-2; Sequence=VSP_026409; Note=No experimental confirmation available;
TISSUE SPECIFICITY: Present at highest levels in testis, where it is enriched in spermatogonia and pachytene cells (at protein level).
DEVELOPMENTAL STAGE: Expressed in developing brain, mammary bud, thymus, teeth, whisker follicle, intervertebral disks, olfactory epithelium, eye, stomach and limbs.
DOMAIN: Both the JmjC domain and the JmjN domain are required for enzymatic activity.
DOMAIN: The 2 first PHD-type zinc finger domains are required for transcription repression activity (By similarity).
SIMILARITY: Belongs to the JARID1 histone demethylase family.
SIMILARITY: Contains 1 ARID domain.
SIMILARITY: Contains 1 JmjC domain.
SIMILARITY: Contains 1 JmjN domain.
SIMILARITY: Contains 3 PHD-type zinc fingers. Sequence=BAD90482.1; Type=Erroneous initiation;
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| Map of ordered and disordered regions |
Note: 'Mouse' over a region to see the start and stop residues. Click on a region to see detailed information.
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| Region 1 | | Type: | Disordered | | Name: | Loop L1 of ARID domain | | Location: | 115 - 128 | | Length: | 14 | | Region sequence: |
GSTLKIPHVERKIL | | Modification type: | Engineered
Fragment
| | PDB: | 2EQY:A | | Structural/functional type: | Function arises from the disordered state
| | Functional classes: | Molecular assembly
| | Functional subclasses: | Protein-DNA binding
| Detection methods:
- Nuclear magnetic resonance (NMR) (298 K; pH: 7; 13C-15N protein 0.77 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02 %; 90% H2O/10% D2O (solvent system))
| References:
- Tanabe, W, Suzuki, S, Muto, Y, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S. "Solution structure of the ARID domain of Jarid1b protein. Primary reference of PDB structure 2EQY: Solution structure of the ARID domain of Jarid1b protein. RIKEN Structural Genomics/Proteomics Initiative. PDB citation." 2007.
| Comments:
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| Region 2 | | Type: | Disordered | | Name: | Loop L2 of ARID domain | | Location: | 159 - 164 | | Length: | 6 | | Region sequence: |
MGFAPG | | Modification type: | Engineered
Fragment
| | PDB: | 2EQY:A | | Structural/functional type: | Function arises from the disordered state
| | Functional classes: | Molecular assembly
| | Functional subclasses: | Protein-DNA binding
| Detection methods:
- Nuclear magnetic resonance (NMR) (298 K; pH: 7; 13C-15N protein 0.77 mM; 90% H2O/10% D2O (solvent system); d-DTT 1 mM; d-Tris-HCl 20 mM; NaCl 100 mM; NaN3 0.02 )
| References:
- Tanabe, W, Suzuki, S, Muto, Y, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S. "Solution structure of the ARID domain of Jarid1b protein. Primary reference of PDB structure 2EQY: Solution structure of the ARID domain of Jarid1b protein. RIKEN Structural Genomics/Proteomics Initiative. PDB citation." 2007.
| Comments:
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| Region 3 | | Type: | Disordered | | Name: | C-tail of ARID domain | | Location: | 178 - 208 | | Length: | 31 | | Region sequence: |
ILNPYNLFLSGDSLRCLQKPNLTSDTKDKEY | | Modification type: | Engineered
Fragment
| | PDB: | 2EQY:A | | Structural/functional type: | Function arises from the disordered state
| | Functional classes: | Molecular assembly
| | Functional subclasses: | Protein-DNA binding
| Detection methods:
- Nuclear magnetic resonance (NMR) (298 K; pH: 7; 13C-15N protein 0.77 mM; 90% H2O/10% D2O (solvent system); d-DTT 1 mM; d-Tris-HCl 20 mM; NaCl 100 mM; NaN3 0.02 mM)
| References:
- Tanabe, W, Suzuki, S, Muto, Y, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S. "Solution structure of the ARID domain of Jarid1b protein. Primary reference of PDB structure 2EQY: Solution structure of the ARID domain of Jarid1b protein. RIKEN Structural Genomics/Proteomics Initiative. PDB citation." 2007.
| Comments:
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| Comments |
The entire ARID domain (aa 97-187 per UniProt) is highly conserved. See also, DP00712 Human JARID1B for additional disorder information.
AV sent to Dr. Muto 6/19/2012
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