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Protein

Lysine-specific demethylase lid

Gene

lid

Organism
Drosophila melanogaster (Fruit fly)
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. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Specifically demethylates trimethylated H3 'Lys-4'. Required for the correct regulation of homeotic genes during development. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. Regulates the expression of clock-controlled genes including tim, per and cry.5 Publications

Cofactori

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

Enzyme regulationi

Inhibited by DM.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi637Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi640Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi725Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri448 – 498PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri1293 – 1354PHD-type 2PROSITE-ProRule annotationAdd BLAST62
Zinc fingeri1753 – 1808PHD-type 3PROSITE-ProRule annotationAdd BLAST56

GO - Molecular functioni

GO - Biological processi

  • chromatin organization Source: FlyBase
  • circadian regulation of gene expression Source: UniProtKB
  • histone demethylation Source: UniProtKB
  • histone H3-K4 demethylation Source: FlyBase
  • histone H3-K4 demethylation, trimethyl-H3-K4-specific Source: FlyBase
  • histone H3-K9 acetylation Source: FlyBase
  • karyosome formation Source: FlyBase
  • larval somatic muscle development Source: FlyBase
  • locomotor rhythm Source: FlyBase
  • male germ-line stem cell population maintenance Source: FlyBase
  • negative regulation of stem cell differentiation Source: FlyBase
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • regulation of JAK-STAT cascade Source: FlyBase
  • synaptonemal complex organization Source: FlyBase
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Developmental protein, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi1.14.11.B2. 1994.
ReactomeiR-DME-8866911. TFAP2 (AP-2) family regulates transcription of cell cycle factors.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase lid (EC:1.14.11.-)
Alternative name(s):
Histone demethylase lid
Jumonji/ARID domain-containing protein lid
Protein little imaginal disks
Retinoblastoma-binding protein 2 homolog
Gene namesi
Name:lid
ORF Names:CG9088
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 2L

Organism-specific databases

FlyBaseiFBgn0031759. lid.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation1 Publication

GO - Cellular componenti

  • nucleus Source: UniProtKB
  • Sin3-type complex Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi637H → A: Abolishes enzymatic activity; when associated with A-536. 1 Publication1
Mutagenesisi639E → A: Abolishes enzymatic activity; when associated with A-534. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002924211 – 1838Lysine-specific demethylase lidAdd BLAST1838

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei323Phosphothreonine1 Publication1
Modified residuei1422Phosphoserine1 Publication1
Modified residuei1433Phosphoserine1 Publication1
Modified residuei1474Phosphoserine1 Publication1
Modified residuei1635Phosphoserine1 Publication1
Modified residuei1640Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9VMJ7.
PRIDEiQ9VMJ7.

PTM databases

iPTMnetiQ9VMJ7.

Expressioni

Gene expression databases

BgeeiFBgn0031759.
ExpressionAtlasiQ9VMJ7. baseline.
GenevisibleiQ9VMJ7. DM.

Interactioni

Subunit structurei

Interacts with DM. Part of a complex containing Lid, DM and Ash2.1 Publication

Protein-protein interaction databases

BioGridi60002. 25 interactors.
DIPiDIP-29330N.
IntActiQ9VMJ7. 6 interactors.
MINTiMINT-1672742.
STRINGi7227.FBpp0297914.

Structurei

Secondary structure

11838
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi217 – 219Combined sources3
Helixi227 – 240Combined sources14
Turni241 – 243Combined sources3
Turni252 – 254Combined sources3
Helixi259 – 269Combined sources11
Helixi272 – 278Combined sources7
Helixi281 – 287Combined sources7
Helixi294 – 315Combined sources22
Turni433 – 436Combined sources4
Beta strandi443 – 446Combined sources4
Turni452 – 455Combined sources4
Helixi460 – 462Combined sources3
Beta strandi463 – 465Combined sources3
Beta strandi472 – 474Combined sources3
Turni475 – 477Combined sources3
Beta strandi478 – 480Combined sources3
Helixi493 – 496Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LM1NMR-A214-320[»]
2MIQNMR-A414-504[»]
ProteinModelPortaliQ9VMJ7.
SMRiQ9VMJ7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini161 – 202JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini226 – 316ARIDPROSITE-ProRule annotationAdd BLAST91
Domaini591 – 757JmjCPROSITE-ProRule annotationAdd BLAST167

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili960 – 1049Sequence analysisAdd BLAST90

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi16 – 23Poly-Gly8
Compositional biasi1415 – 1418Poly-Gln4
Compositional biasi1454 – 1462Poly-Asp9
Compositional biasi1697 – 1719Asn-richAdd BLAST23

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 fingeri448 – 498PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri1293 – 1354PHD-type 2PROSITE-ProRule annotationAdd BLAST62
Zinc fingeri1753 – 1808PHD-type 3PROSITE-ProRule annotationAdd BLAST56

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
InParanoidiQ9VMJ7.
KOiK11446.
OMAiQVFCICR.
OrthoDBiEOG091G0RFR.
PhylomeDBiQ9VMJ7.

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.

Q9VMJ7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAKTEADNT TAANSGGGGV GSGTSSGGGA SANGTATPAR RLRTRNSTGN
60 70 80 90 100
GTNSGSESVK KSNANDEPST PVTPAGATGS HTHAPPGISP AVMERPMPSV
110 120 130 140 150
PMNHASSSVS ASKKYHNSCP HPTPTPAPTG HKKSVHTQPH SSNKFDQGKN
160 170 180 190 200
EEFHFDTPPE CPVFRPTTEE FKNPLAYISK IRSIAEKCGI AKILPPATWS
210 220 230 240 250
PPFAVDVDKL RFVPRVQRLN ELEAKTRVKL NFLDQIAKFW ELQGSSLKIP
260 270 280 290 300
MVERKALDLY TLHRIVQEEG GMEQTTKDRK WAKVANRMQY PSSKSVGATL
310 320 330 340 350
KAHYERILHP FEVYTSGKVL GPTPTSSGSG STPVKLEDGG GTDYKAHEIP
360 370 380 390 400
TRQQIAPPNE TNTRRSKRFG NSNASCGLSG VTPTTKPSAG VFVKTETKEE
410 420 430 440 450
FKRDLLSSFN AVNSGGSPLA TGTTANTRGA SQKKGGEPPA LIVDPLMKYI
460 470 480 490 500
CHICNRGDVE ESMLLCDGCD DSYHTFCLLP PLTSIPKGEW LCPRCVVEEV
510 520 530 540 550
SKPQEAFGFE QAEREYTLQQ FGQMADQFKQ EYFRKPVHLV PTEMVEREFW
560 570 580 590 600
RIVSSIDEDV TVEYGADLHT MDHGSGFPTK SSLYLLPGDQ EYAESSWNLN
610 620 630 640 650
NLPLLEDSIL GHINADISGM NAPWMYVGMC FAAFCWHNED HWSYSINYLH
660 670 680 690 700
WGEPKTWYGV PGSCAEQFEE TMKQAAPELF SSQPDLLHQL VTIMNPNILM
710 720 730 740 750
NNRVPVFRTD QHAGEFVITF PRAYHAGFNQ GYNFAEAVNF APADWLKMGR
760 770 780 790 800
ECVNHYSMLR RFCVFSHDEL VCKMALEPAK LTFGIATACY IDMAEMVDTE
810 820 830 840 850
KKLRKSLLEW GVTRAERRAF ELVNDDERHC QECNTTCFLS AVACECNDKL
860 870 880 890 900
IVCLRHYTVL CGCAPEKHTL IYRYTLDEMP LMLQKLKVKA HSFERWLSRC
910 920 930 940 950
RDIVDAHTPT SVTLQELQEL CKEAETKKFP SSLLIDRLNA AAVEAEKCVT
960 970 980 990 1000
VIQQLGINKV RTRSDHNQEA AQYKLTMEEL ELFVQEIDNL CCIIDEGASV
1010 1020 1030 1040 1050
RELLVLGKQF VERSESQLQL SLESLEESEL ETLINEGSSL RIELQQLDLL
1060 1070 1080 1090 1100
QKRLKQCKWY KRSQGLRETS SKLTYQDVKN LLHIAAADLD PTDPYVDKEM
1110 1120 1130 1140 1150
RKLQQIGADI EAWESQAAKY FRRLTQQHEL GEIEQFLKSA SDINGQVPSH
1160 1170 1180 1190 1200
GLLKDALRKA REWLRAVEQL QQNNHVTYCH TLEAMIERGL NIPIQLEELS
1210 1220 1230 1240 1250
RMQGHLNSAH QWKDNTACAF LKKGTFYTLL EVLMPRSDAI NIDSDLKPRF
1260 1270 1280 1290 1300
QDDFLKEKNP AEIVASFKHA EEQELLDMRE LRRQNMNKNP MRDMFCLCKS
1310 1320 1330 1340 1350
EFRNLMFNCQ LCRDWFHEDC VPPPSATNQN GIVNGGSGPG TNRPKWLCPS
1360 1370 1380 1390 1400
CVRSKRPRLE TILPLLVQLQ QLPIRLPEDE ALRCLAERAM NWQDRARKAL
1410 1420 1430 1440 1450
SSPDVSAAQE AIMAQQQQKR RSEGGAGVGN ISSPRKPRRR GSLTKEASGS
1460 1470 1480 1490 1500
TESDADDDDD EDECRLRIVE DNFSNDEDEP RTAPATSTVN SDLLKLLSDS
1510 1520 1530 1540 1550
EIENLLDLMM EGDLLEVSLD ETQELWRILE TMPPTLLQAE AMERVVQYMQ
1560 1570 1580 1590 1600
RQRQQHTNPL PTSGAEDSND SLMVQNSPNS NSNSGGATGS ASNSGRNKKR
1610 1620 1630 1640 1650
RSNDTGGNSA VPRKKQSTPK QTPGKKGSAA AARKSDAKAS PAASTTPGAD
1660 1670 1680 1690 1700
ADAENKQANG GNTNSSTGSG GGNSATTTPT PGSTHKKRKR TSTTATNNNN
1710 1720 1730 1740 1750
NNNNNSTNNS NSSTNLNSNT TSGQGAATGG NNATGGQKKH AQRSQQAAQE
1760 1770 1780 1790 1800
DDEEECRAEN CHKPTGREVD WVQCDGGCNE WFHMYCVGLN RSQIKPDDDY
1810 1820 1830
ICIRCTKTVA IGTQGSGHSM SVASTTTPGK QRAVQSAR
Length:1,838
Mass (Da):203,993
Last modified:May 1, 2000 - v1
Checksum:iE01BDB89027F9F50
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014134 Genomic DNA. Translation: AAF52319.1.
AY095051 mRNA. Translation: AAM11379.1.
AE014134 Genomic DNA. Translation: AAN10569.1.
RefSeqiNP_001245908.1. NM_001258979.2.
NP_001245909.1. NM_001258980.1.
NP_001245910.1. NM_001258981.2.
NP_001285649.1. NM_001298720.1.
NP_523486.1. NM_078762.6.
NP_723140.1. NM_164671.1.
UniGeneiDm.2779.

Genome annotation databases

EnsemblMetazoaiFBtr0079231; FBpp0078862; FBgn0031759.
FBtr0079232; FBpp0078863; FBgn0031759.
FBtr0307069; FBpp0297912; FBgn0031759.
FBtr0307070; FBpp0297913; FBgn0031759.
FBtr0307071; FBpp0297914; FBgn0031759.
FBtr0345336; FBpp0311492; FBgn0031759.
GeneIDi33837.
KEGGidme:Dmel_CG9088.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014134 Genomic DNA. Translation: AAF52319.1.
AY095051 mRNA. Translation: AAM11379.1.
AE014134 Genomic DNA. Translation: AAN10569.1.
RefSeqiNP_001245908.1. NM_001258979.2.
NP_001245909.1. NM_001258980.1.
NP_001245910.1. NM_001258981.2.
NP_001285649.1. NM_001298720.1.
NP_523486.1. NM_078762.6.
NP_723140.1. NM_164671.1.
UniGeneiDm.2779.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LM1NMR-A214-320[»]
2MIQNMR-A414-504[»]
ProteinModelPortaliQ9VMJ7.
SMRiQ9VMJ7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi60002. 25 interactors.
DIPiDIP-29330N.
IntActiQ9VMJ7. 6 interactors.
MINTiMINT-1672742.
STRINGi7227.FBpp0297914.

PTM databases

iPTMnetiQ9VMJ7.

Proteomic databases

PaxDbiQ9VMJ7.
PRIDEiQ9VMJ7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0079231; FBpp0078862; FBgn0031759.
FBtr0079232; FBpp0078863; FBgn0031759.
FBtr0307069; FBpp0297912; FBgn0031759.
FBtr0307070; FBpp0297913; FBgn0031759.
FBtr0307071; FBpp0297914; FBgn0031759.
FBtr0345336; FBpp0311492; FBgn0031759.
GeneIDi33837.
KEGGidme:Dmel_CG9088.

Organism-specific databases

CTDi33837.
FlyBaseiFBgn0031759. lid.

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
InParanoidiQ9VMJ7.
KOiK11446.
OMAiQVFCICR.
OrthoDBiEOG091G0RFR.
PhylomeDBiQ9VMJ7.

Enzyme and pathway databases

BRENDAi1.14.11.B2. 1994.
ReactomeiR-DME-8866911. TFAP2 (AP-2) family regulates transcription of cell cycle factors.

Miscellaneous databases

GenomeRNAii33837.
PROiQ9VMJ7.

Gene expression databases

BgeeiFBgn0031759.
ExpressionAtlasiQ9VMJ7. baseline.
GenevisibleiQ9VMJ7. DM.

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 nameiKDM5_DROME
AccessioniPrimary (citable) accession number: Q9VMJ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.