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Protein

Lysine-specific demethylase rbr-2

Gene

rbr-2

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:17320161). Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20' (PubMed:17320161). Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4' (PubMed:17320161). Required for normal longevity of the soma in a germline-dependent manner (PubMed:20555324, PubMed:22212395). Implicated in the epigenetic inheritance of lifespan over several generations (PubMed:22012258). Involved in larval development and vulva formation (PubMed:17320161).4 Publications

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi514Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi517Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi602Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri319 – 371PHD-type 1PROSITE-ProRule annotationAdd BLAST53
Zinc fingeri1203 – 1257PHD-type 2PROSITE-ProRule annotationAdd BLAST55
Zinc fingeri1411 – 1466PHD-type 3PROSITE-ProRule annotationAdd BLAST56

GO - Molecular functioni

GO - Biological processi

  • determination of adult lifespan Source: WormBase
  • histone H3-K4 demethylation Source: WormBase
  • regulation of transcription, DNA-templated Source: WormBase
  • regulation of vulval development Source: WormBase
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase
Biological processTranscription, Transcription regulation
LigandIron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase rbr-2
Alternative name(s):
Histone demethylase rbr-2 (EC:1.14.11.-)
Jumonji/ARID domain-containing protein rbr-2
Gene namesi
Name:rbr-2
ORF Names:ZK593.4
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome IV

Organism-specific databases

WormBaseiZK593.4a; CE35704; WBGene00004319; rbr-2.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: WormBase

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

RNAi-mediated knockdown decreases lifespan in wild type worms with an intact germline (PubMed:20555324). Results in extended lifespan when egg production is inhibited by the addition of floxuridine (FUDR) or in a glp-1 mutant background which lacks a germline (PubMed:22212395, PubMed:20555324).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002924201 – 1477Lysine-specific demethylase rbr-2Add BLAST1477

Proteomic databases

PaxDbiQ23541.
PeptideAtlasiQ23541.
PRIDEiQ23541.

Expressioni

Gene expression databases

BgeeiWBGene00004319.
ExpressionAtlasiQ23541. baseline.

Interactioni

Protein-protein interaction databases

BioGridi43086. 3 interactors.
IntActiQ23541. 26 interactors.
STRINGi6239.ZK593.4.

Structurei

3D structure databases

ProteinModelPortaliQ23541.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini56 – 97JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini121 – 218ARIDPROSITE-ProRule annotationAdd BLAST98
Domaini468 – 634JmjCPROSITE-ProRule annotationAdd BLAST167

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili874 – 926Sequence analysisAdd BLAST53

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi309 – 315Poly-Asp7

Sequence similaritiesi

Belongs to the JARID1 histone demethylase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri319 – 371PHD-type 1PROSITE-ProRule annotationAdd BLAST53
Zinc fingeri1203 – 1257PHD-type 2PROSITE-ProRule annotationAdd BLAST55
Zinc fingeri1411 – 1466PHD-type 3PROSITE-ProRule annotationAdd BLAST56

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000113216.
InParanoidiQ23541.
KOiK11446.
OMAiKAVGSHI.
OrthoDBiEOG091G0RFR.
PhylomeDBiQ23541.

Family and domain databases

Gene3Di3.30.40.10. 3 hits.
InterProiView protein in InterPro
IPR001606. 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.
PfamiView protein in Pfam
PF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 1 hit.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
SMARTiView protein in SMART
SM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 3 hits.
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 3 hits.
PROSITEiView protein in PROSITE
PS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.

Sequencei

Sequence statusi: Complete.

Q23541-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRARRQENSI STPSAPSTST SPRKKASIGN SRSKNHGSKM EMYDQFYKKF
60 70 80 90 100
VRPPMAPIYY PTEEEFSDPI EYVAKIRHEA EKFGVVKIVP PANFKPPFAI
110 120 130 140 150
DKEAFTFRPR TQKLNEVEAI VKEKHTFIDR LINFNRYSGL TFEFPVDRDG
160 170 180 190 200
NIVDLYRLHR IVQNFGGCEE VNEDEKWRDV AREYLPKEQM ARGVPSAFIN
210 220 230 240 250
LIRSHYNLHI EPFNRNLKEK AMKNDDESDD EMEELKHKYQ HHHGTMRTEI
260 270 280 290 300
EVPNDKTTEG GEDECPVSMQ SGRRRSKNKK ASSSRKTLGT SSKKNSTRGR
310 320 330 340 350
KNKKKAEGDD DDDEDPMDQV FCVACNEGKD EDLLLLCDID GCNNGRHTYC
360 370 380 390 400
CDPVLDEVPE GEWRCPKCIE SEDAKIGLDW GFYDADTEYN LNSFTEFANK
410 420 430 440 450
WKCDYFGVKD VSQVSCDAVE RSFWKNVISH ENPVSVKYGA DLITSRVGSG
460 470 480 490 500
FPRKEDKHTG PDLKLKQQYA SHAWNLNNMP VLRESVLSHF NTGISGMMVP
510 520 530 540 550
WVYVGMCFST FCWHTEDHWT YSVNYNHFGE RKIWYGVGGE DAEKFEDALK
560 570 580 590 600
KIAPGLTGRQ RDLFHHMTTA ANPHLLRSLG VPIHSVHQNA GEFVITFPRA
610 620 630 640 650
YHAGFNEGLN FAEAVNFAPI DWLSKGRECV ESYSNVRRYL VFSHDELLFK
660 670 680 690 700
MVEAMDKLGI SMSLATHEEL IRIYEKQKML RELLARLGVS NRQMQQVMFE
710 720 730 740 750
KIPDEQRSCR FCKTTLFMCA LVCNKHKKMT CVEHHDHLCN SCTTKDYRYQ
760 770 780 790 800
YRFELDQLNN MCDELGKRTV NYNGWKEESD EMLEEEGKPK LERIEEFIDS
810 820 830 840 850
AKQNKYPQTD QVHKLITIRH TAKSAIEKAN QLLFKKVRTR TKTRCQRADT
860 870 880 890 900
RTDTEGVRSL IEQMQAMDCN LTVIIDKLEK WMEQVEMWRN RAKDAIYREQ
910 920 930 940 950
EYSKEEIEKI IEEGDEYDIK LEEIDELRKV IQMKDWSDRA RKVTTWKATP
960 970 980 990 1000
DMEKDIDFEY KLRYASSDIL SLIRDSPRNP TDGTSKLVFE LQQMLRDANT
1010 1020 1030 1040 1050
LEVIANNFCE NPALDQLQSI WQSLRETDWF YEKYINMVRY EIIHVAKIKS
1060 1070 1080 1090 1100
MIDAAIPVLS EFDLKTQLQK IVNVEITLSK AAEISKAFET SKCLNGSEEH
1110 1120 1130 1140 1150
LGILDMISTM NAFTQRIAIL FKPNNAYHNL FEILSERDDL TPLAEGQTIP
1160 1170 1180 1190 1200
LYFQGGAVHP SDEWHQMKEF ESLDQIVHHQ SSLREMQMRI FEKVKQANSA
1210 1220 1230 1240 1250
RGLEACSCLG FNKSDDSEST LTCIMCDSEF HVRCCEWSPF LEKLPEGCFL
1260 1270 1280 1290 1300
CVRCLRGQRP VIDDVTTALN GTPSGCLETH LVRNLIQKTR GITQNLMEAA
1310 1320 1330 1340 1350
NKRKSGESSD DICKIALFDW LSCEILNPNG LPKARELISE FYMEYLQKQS
1360 1370 1380 1390 1400
SAALELKNRP VRSKPSVSLF DPKITAKRKR PSVSHKETSK KSRKRQSQAS
1410 1420 1430 1440 1450
PSEYYEDESE FKSCQARACL KPYGDSVNWV MCEAGCKNWF HVICLGFTLR
1460 1470
EINDMHEYRC SSCLDHADSP TSSVSTD
Length:1,477
Mass (Da):170,791
Last modified:July 5, 2004 - v2
Checksum:iE2539E727C6E72D7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69385 Genomic DNA. Translation: CAA93426.2.
PIRiT27924.
RefSeqiNP_502032.2. NM_069631.6.
UniGeneiCel.6207.

Genome annotation databases

EnsemblMetazoaiZK593.4a; ZK593.4a; WBGene00004319.
GeneIDi177985.
KEGGicel:CELE_ZK593.4.
UCSCiZK593.4. c. elegans.

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.

Entry informationi

Entry nameiKDM5_CAEEL
AccessioniPrimary (citable) accession number: Q23541
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: July 5, 2004
Last modified: July 5, 2017
This is version 126 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families