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Protein

Lysine-specific demethylase 5B

Gene

KDM5B

Organism
Gallus gallus (Chicken)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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. May repress the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2.By similarity

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi474Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi477Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi562Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri284 – 334PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri1151 – 1199PHD-type 2PROSITE-ProRule annotationAdd BLAST49
Zinc fingeri1462 – 1516PHD-type 3PROSITE-ProRule annotationAdd BLAST55

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase, Repressor

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 5B (EC:1.14.11.-)
Alternative name(s):
Histone demethylase JARID1B
Jumonji/ARID domain-containing protein 1B
Gene namesi
Name:KDM5B
Synonyms:JARID1B
ORF Names:RCJMB04_9d3
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
Proteomesi
  • UP000000539 Componenti: Unplaced

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002924141 – 1522Lysine-specific demethylase 5BAdd BLAST1522

Proteomic databases

PaxDbiQ5F3R2.

Interactioni

Protein-protein interaction databases

STRINGi9031.ENSGALP00000040038.

Structurei

3D structure databases

ProteinModelPortaliQ5F3R2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini10 – 51JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini75 – 165ARIDPROSITE-ProRule annotationAdd BLAST91
Domaini428 – 594JmjCPROSITE-ProRule annotationAdd BLAST167

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1409 – 1414Poly-Lys6
Compositional biasi1422 – 1425Poly-Ser4

Domaini

Both the JmjC domain and the JmjN domain are required for enzymatic activity.By similarity
The 2 first PHD-type zinc finger domains are required for transcription repression 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 3 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri284 – 334PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri1151 – 1199PHD-type 2PROSITE-ProRule annotationAdd BLAST49
Zinc fingeri1462 – 1516PHD-type 3PROSITE-ProRule annotationAdd BLAST55

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiQ5F3R2.
KOiK11446.
PhylomeDBiQ5F3R2.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 3 hits.
InterProiIPR001606. ARID_dom.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR013637. Lys_sp_deMease-like_dom.
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. 3 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]
SMARTiSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 3 hits.
[Graphical view]
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 3 hits.
PROSITEiPS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5F3R2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEFLPPPEC PVFEPSWEEF ADPFAFIHKI RPIAEQTGIC KVRPPPDWQP
60 70 80 90 100
PFACDVDKLH FTPRIQRLNE LEAQTRVKLN FLDQIAKFWE LQGCTLKIPH
110 120 130 140 150
VERKILDLFQ LNRLVAEEGG FDVVCKERKW TKIATRMGFA PGKAVGSHIR
160 170 180 190 200
AHYERILYPY NLFQSGASLL CLQKPDLTSD TKDKEYKPHD IPQRQSVQPS
210 220 230 240 250
ESCPPARRAK RLRAEATNIK TESDSPEVRT HNLRRRMGCA PPKCENEKET
260 270 280 290 300
YSAVKLAEKR EHAGEQERDK AKARSKKPTS AVDLYVCLLC GSGNDEDRLL
310 320 330 340 350
LCDGCDDSYH TFCLIPPLHD VPKGDWRCPQ CLAQECNKPQ EAFGFEQAAR
360 370 380 390 400
DYTLRTFGEM ADAFKSDYFN MPVHMVPTEL VEKEFWRLVS TIEEDVTVEY
410 420 430 440 450
GADIASKEFG SGFPVRDGKF KVRPEEEEYL DSGWNLNNMP VMEQSVLAHI
460 470 480 490 500
TADICGMKLP WLYVGMCFSS FCWHIEDHWS YSINYLHWGE PKTWYGAPGY
510 520 530 540 550
AAEQLEDVMK KLAPELFESQ PDLLHQLVTI MNPNTLMAHG VPVYRTNQCA
560 570 580 590 600
GEFVITFPRA YHSGFNQGFN FAEAVNFCTV DWLPLGRQCI EHYRLLSRYC
610 620 630 640 650
VFSHDEMICK MASKADILDV VVASTVQKDM AIMIDDEKML REKVQKLGVT
660 670 680 690 700
DSERVAFELF PDDERQCYKC KTTCFMSAVY CPCKPGLLVC LYHVEDLCSC
710 720 730 740 750
PTYQYKLGYR YTLEELYPMM NALKMRAESY NEWASNVNEA LEAKISNKRS
760 770 780 790 800
LISFKALIEE SELKKFPDND LLRHLRLVTQ DADKCASVAQ QLLNGKRQTR
810 820 830 840 850
YRSGGGKCPN QLTVNELRLF VRQLYALPCV LSQTPLLKDL LDRVEAFQQQ
860 870 880 890 900
SQKLLSEEMP SAAELQELLD VSFDFDVDLP QLAELRVRLE QARWLEDVQM
910 920 930 940 950
ASAEQNSLTL DDMRRLIDSG VGLAPYPAVE KAMAKLQELL TVSEHWDDKA
960 970 980 990 1000
RNLIKARPRQ SLSSLVVAVK EIEEIPAYLP SGAALKDAVQ KAQDWLQEVE
1010 1020 1030 1040 1050
ALQVGGRVPV LDTLVELVTR GRSIPVHLDY LPRLESLVAE VQAWKECAAN
1060 1070 1080 1090 1100
TFLCENSPYS LLEVLCPRCD IGTLGLKRKQ KKLKEPMPSG KKRSTKLESL
1110 1120 1130 1140 1150
SDLERALSES KDTASAMATL GEARLKEMEA LRSLRAANEG KVLCSEEDAE
1160 1170 1180 1190 1200
LKVCVCQKEP AAPMIQCELC RGFFHTGCVS VPHALQGPRV WLCPQCRRSE
1210 1220 1230 1240 1250
KPPLEKILPL LASLQRIRVR LPEGDALRYM IERTVNWQHR AQQMLYSGNL
1260 1270 1280 1290 1300
KLLQDKVGSG LLYNRWQSTA GPLPETNKVS QTIGAMSFSM PHDWDNRTIY
1310 1320 1330 1340 1350
LHSPFSTGQQ CIPLHVVSTE LDELMMEAQL LQVSLPEIQE LYQILFTKQS
1360 1370 1380 1390 1400
PSLQAEQKPS VGPSNEKSEC CRGKKDGMSY MERKLKRRFE RESFCDEKRA
1410 1420 1430 1440 1450
RVRKMRTPKK KKLKLSHTKD VSSSSRMERE RERLLEAQRS SESHLVPSDT
1460 1470 1480 1490 1500
SFSEQEDSED EDAICPAVTC LQPEGEEVDW VQCDGSCNQW FHQVCVGISP
1510 1520
EMAEKEDYIC ASCAGKGSPY RK
Length:1,522
Mass (Da):173,462
Last modified:March 15, 2005 - v1
Checksum:i69148B3145D7C010
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ851588 mRNA. Translation: CAH65222.1.
RefSeqiNP_001026200.1. NM_001031029.1.
UniGeneiGga.7752.

Genome annotation databases

EnsembliENSGALT00000071675; ENSGALP00000056668; ENSGALG00000038948.
GeneIDi421168.
KEGGigga:421168.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ851588 mRNA. Translation: CAH65222.1.
RefSeqiNP_001026200.1. NM_001031029.1.
UniGeneiGga.7752.

3D structure databases

ProteinModelPortaliQ5F3R2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9031.ENSGALP00000040038.

Proteomic databases

PaxDbiQ5F3R2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000071675; ENSGALP00000056668; ENSGALG00000038948.
GeneIDi421168.
KEGGigga:421168.

Organism-specific databases

CTDi10765.

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiQ5F3R2.
KOiK11446.
PhylomeDBiQ5F3R2.

Miscellaneous databases

PROiQ5F3R2.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 3 hits.
InterProiIPR001606. ARID_dom.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR013637. Lys_sp_deMease-like_dom.
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. 3 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]
SMARTiSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 3 hits.
[Graphical view]
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 3 hits.
PROSITEiPS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKDM5B_CHICK
AccessioniPrimary (citable) accession number: Q5F3R2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: March 15, 2005
Last modified: November 30, 2016
This is version 73 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.