Q9VMJ7 (KDM5_DROME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	lid
ORF Names:	CG9088

Organism

Drosophila melanogaster (Fruit fly)

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Arthropoda › Hexapoda › Insecta › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Ephydroidea › Drosophilidae › Drosophila › Sophophora

Protein attributes

Sequence length	1838 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.4 Ref.5 Ref.7 Ref.8
Cofactor	Binds 1 Fe2+ ion per subunit By similarity.
Enzyme regulation	Inhibited by DM. Ref.5
Subunit structure	Interacts with DM. Part of a complex containing Lid, DM and Ash2. Ref.5
Subcellular location	Nucleus Ref.5.
Sequence similarities	Belongs to the JARID1 histone demethylase family. Contains 1 ARID domain. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 3 PHD-type zinc fingers.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Coiled coil Repeat Zinc-finger
Ligand	Iron Metal-binding Zinc
Molecular function	Chromatin regulator Developmental protein Dioxygenase Oxidoreductase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	multicellular organismal development Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of transcription, DNA-dependent Inferred from mutant phenotype Ref.5. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	Sin3-type complex Inferred from direct assay. Source: FlyBase
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro histone acetyltransferase activity (H3-K9 specific) Inferred from mutant phenotype. Source: FlyBase histone demethylase activity (H3-trimethyl-K4 specific) Inferred from mutant phenotype. Source: FlyBase oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction Ref.5. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1838	1838	Lysine-specific demethylase lid		PRO_0000292421
Regions
	Domain	161 – 202	42	JmjN
	Domain	226 – 316	91	ARID
	Domain	591 – 757	167	JmjC
	Zinc finger	448 – 498	51	PHD-type 1
	Zinc finger	1293 – 1354	62	PHD-type 2
	Zinc finger	1753 – 1808	56	PHD-type 3
	Coiled coil	960 – 1049	90	Potential
	Compositional bias	16 – 23	8	Poly-Gly
	Compositional bias	1415 – 1418	4	Poly-Gln
	Compositional bias	1454 – 1462	9	Poly-Asp
	Compositional bias	1697 – 1719	23	Asn-rich
Sites
	Metal binding	637	1	Iron; catalytic By similarity
	Metal binding	640	1	Iron; catalytic By similarity
	Metal binding	725	1	Iron; catalytic By similarity
Amino acid modifications
	Modified residue	323	1	Phosphothreonine Ref.9
	Modified residue	1422	1	Phosphoserine Ref.9
	Modified residue	1433	1	Phosphoserine Ref.9
	Modified residue	1474	1	Phosphoserine Ref.6
	Modified residue	1635	1	Phosphoserine Ref.9
	Modified residue	1640	1	Phosphoserine Ref.9
Experimental info
	Mutagenesis	637	1	H → A: Abolishes enzymatic activity; when associated with A-536. Ref.5
	Mutagenesis	639	1	E → A: Abolishes enzymatic activity; when associated with A-534. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Q9VMJ7 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: E01BDB89027F9F50	FASTA	1,838	203,993
	10 20 30 40 50 60 MSAKTEADNT TAANSGGGGV GSGTSSGGGA SANGTATPAR RLRTRNSTGN GTNSGSESVK 70 80 90 100 110 120 KSNANDEPST PVTPAGATGS HTHAPPGISP AVMERPMPSV PMNHASSSVS ASKKYHNSCP 130 140 150 160 170 180 HPTPTPAPTG HKKSVHTQPH SSNKFDQGKN EEFHFDTPPE CPVFRPTTEE FKNPLAYISK 190 200 210 220 230 240 IRSIAEKCGI AKILPPATWS PPFAVDVDKL RFVPRVQRLN ELEAKTRVKL NFLDQIAKFW 250 260 270 280 290 300 ELQGSSLKIP MVERKALDLY TLHRIVQEEG GMEQTTKDRK WAKVANRMQY PSSKSVGATL 310 320 330 340 350 360 KAHYERILHP FEVYTSGKVL GPTPTSSGSG STPVKLEDGG GTDYKAHEIP TRQQIAPPNE 370 380 390 400 410 420 TNTRRSKRFG NSNASCGLSG VTPTTKPSAG VFVKTETKEE FKRDLLSSFN AVNSGGSPLA 430 440 450 460 470 480 TGTTANTRGA SQKKGGEPPA LIVDPLMKYI CHICNRGDVE ESMLLCDGCD DSYHTFCLLP 490 500 510 520 530 540 PLTSIPKGEW LCPRCVVEEV SKPQEAFGFE QAEREYTLQQ FGQMADQFKQ EYFRKPVHLV 550 560 570 580 590 600 PTEMVEREFW RIVSSIDEDV TVEYGADLHT MDHGSGFPTK SSLYLLPGDQ EYAESSWNLN 610 620 630 640 650 660 NLPLLEDSIL GHINADISGM NAPWMYVGMC FAAFCWHNED HWSYSINYLH WGEPKTWYGV 670 680 690 700 710 720 PGSCAEQFEE TMKQAAPELF SSQPDLLHQL VTIMNPNILM NNRVPVFRTD QHAGEFVITF 730 740 750 760 770 780 PRAYHAGFNQ GYNFAEAVNF APADWLKMGR ECVNHYSMLR RFCVFSHDEL VCKMALEPAK 790 800 810 820 830 840 LTFGIATACY IDMAEMVDTE KKLRKSLLEW GVTRAERRAF ELVNDDERHC QECNTTCFLS 850 860 870 880 890 900 AVACECNDKL IVCLRHYTVL CGCAPEKHTL IYRYTLDEMP LMLQKLKVKA HSFERWLSRC 910 920 930 940 950 960 RDIVDAHTPT SVTLQELQEL CKEAETKKFP SSLLIDRLNA AAVEAEKCVT VIQQLGINKV 970 980 990 1000 1010 1020 RTRSDHNQEA AQYKLTMEEL ELFVQEIDNL CCIIDEGASV RELLVLGKQF VERSESQLQL 1030 1040 1050 1060 1070 1080 SLESLEESEL ETLINEGSSL RIELQQLDLL QKRLKQCKWY KRSQGLRETS SKLTYQDVKN 1090 1100 1110 1120 1130 1140 LLHIAAADLD PTDPYVDKEM RKLQQIGADI EAWESQAAKY FRRLTQQHEL GEIEQFLKSA 1150 1160 1170 1180 1190 1200 SDINGQVPSH GLLKDALRKA REWLRAVEQL QQNNHVTYCH TLEAMIERGL NIPIQLEELS 1210 1220 1230 1240 1250 1260 RMQGHLNSAH QWKDNTACAF LKKGTFYTLL EVLMPRSDAI NIDSDLKPRF QDDFLKEKNP 1270 1280 1290 1300 1310 1320 AEIVASFKHA EEQELLDMRE LRRQNMNKNP MRDMFCLCKS EFRNLMFNCQ LCRDWFHEDC 1330 1340 1350 1360 1370 1380 VPPPSATNQN GIVNGGSGPG TNRPKWLCPS CVRSKRPRLE TILPLLVQLQ QLPIRLPEDE 1390 1400 1410 1420 1430 1440 ALRCLAERAM NWQDRARKAL SSPDVSAAQE AIMAQQQQKR RSEGGAGVGN ISSPRKPRRR 1450 1460 1470 1480 1490 1500 GSLTKEASGS TESDADDDDD EDECRLRIVE DNFSNDEDEP RTAPATSTVN SDLLKLLSDS 1510 1520 1530 1540 1550 1560 EIENLLDLMM EGDLLEVSLD ETQELWRILE TMPPTLLQAE AMERVVQYMQ RQRQQHTNPL 1570 1580 1590 1600 1610 1620 PTSGAEDSND SLMVQNSPNS NSNSGGATGS ASNSGRNKKR RSNDTGGNSA VPRKKQSTPK 1630 1640 1650 1660 1670 1680 QTPGKKGSAA AARKSDAKAS PAASTTPGAD ADAENKQANG GNTNSSTGSG GGNSATTTPT 1690 1700 1710 1720 1730 1740 PGSTHKKRKR TSTTATNNNN NNNNNSTNNS NSSTNLNSNT TSGQGAATGG NNATGGQKKH 1750 1760 1770 1780 1790 1800 AQRSQQAAQE DDEEECRAEN CHKPTGREVD WVQCDGGCNE WFHMYCVGLN RSQIKPDDDY 1810 1820 1830 ICIRCTKTVA IGTQGSGHSM SVASTTTPGK QRAVQSAR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome sequence of Drosophila melanogaster." Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D. , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C. Science 287:2185-2195(2000) [PubMed: 10731132] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Berkeley.
[2]	"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review." Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J. , Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E. Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed: 12537572] [Abstract] Cited for: GENOME REANNOTATION. Strain: Berkeley.
[3]	"A Drosophila full-length cDNA resource." Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M., Celniker S.E. Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002) [PubMed: 12537569] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: Berkeley. Tissue: Embryo.
[4]	"A screen for new trithorax group genes identified little imaginal discs, the Drosophila melanogaster homologue of human retinoblastoma binding protein 2." Gildea J.J., Lopez R., Shearn A. Genetics 156:645-663(2000) [PubMed: 11014813] [Abstract] Cited for: IDENTIFICATION, FUNCTION.
[5]	"The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth." Secombe J., Li L., Carlos L., Eisenman R.N. Genes Dev. 21:537-551(2007) [PubMed: 17311883] [Abstract] Cited for: FUNCTION, ENZYME REGULATION, INTERACTION WITH DM, IDENTIFICATION IN COMPLEX WITH DM AND ASH2, SUBCELLULAR LOCATION, MUTAGENESIS OF HIS-637 AND GLU-639.
[6]	"An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells." Bodenmiller B., Mueller L.N., Pedrioli P.G.A., Pflieger D., Juenger M.A., Eng J.K., Aebersold R., Tao W.A. Mol. Biosyst. 3:275-286(2007) [PubMed: 17372656] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1474, MASS SPECTROMETRY.
[7]	"The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase." Lee N., Zhang J., Klose R.J., Erdjument-Bromage H., Tempst P., Jones R.S., Zhang Y. Nat. Struct. Mol. Biol. 14:341-343(2007) [PubMed: 17351631] [Abstract] Cited for: FUNCTION.
[8]	"The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase." Eissenberg J.C., Lee M.G., Schneider J., Ilvarsonn A., Shiekhattar R., Shilatifard A. Nat. Struct. Mol. Biol. 14:344-346(2007) [PubMed: 17351630] [Abstract] Cited for: FUNCTION.
[9]	"Phosphoproteome analysis of Drosophila melanogaster embryos." Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P. J. Proteome Res. 7:1675-1682(2008) [PubMed: 18327897] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-323; SER-1422; SER-1433; SER-1635 AND SER-1640, MASS SPECTROMETRY. Tissue: Embryo.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE014134 Genomic DNA. Translation: AAF52319.1. AY095051 mRNA. Translation: AAM11379.1. AE014134 Genomic DNA. Translation: AAN10569.1.
RefSeq	NP_523486.1. NM_078762.4. NP_723140.1. NM_164671.1.
UniGene	Dm.2779.
3D structure databases
HSSP	HSSP built from PDB template 1MM2 based on UniProtKB Q14839.
ProteinModelPortal	Q9VMJ7.
SMR	Q9VMJ7. Positions 194-318, 449-774, 1293-1358, 1754-1806.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-29330N.
IntAct	Q9VMJ7. 1 interaction.
MINT	MINT-1672742.
STRING	Q9VMJ7.
Proteomic databases
PRIDE	Q9VMJ7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	FBtr0079231; FBpp0078862; FBgn0031759. FBtr0079232; FBpp0078863; FBgn0031759. FBtr0307069; FBpp0297912; FBgn0031759. FBtr0307070; FBpp0297913; FBgn0031759. FBtr0307071; FBpp0297914; FBgn0031759.
GeneID	33837.
KEGG	dme:Dmel_CG9088.
Organism-specific databases
CTD	33837.
FlyBase	FBgn0031759. lid.
Phylogenomic databases
eggNOG	inNOG07044.
GeneTree	EMGT00050000000371.
InParanoid	Q9VMJ7.
OMA	WRILETM.
OrthoDB	EOG408KPT.
PhylomeDB	Q9VMJ7.
Gene expression databases
ArrayExpress	Q9VMJ7.
Bgee	Q9VMJ7.
Family and domain databases
InterPro	IPR001606. ARID/BRIGHT_DNA-bd. IPR013637. Lys_sp_deMease_like_dom. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR003349. TF_JmjN. 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]
Gene3D	G3DSA:1.10.150.60. ARID. 1 hit. G3DSA:3.30.40.10. Znf_RING/FYVE/PHD. 3 hits.
KO	K11446.
Pfam	PF01388. 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]
SMART	SM00501. BRIGHT. 1 hit. SM00558. JmjC. 1 hit. SM00545. JmjN. 1 hit. SM00249. PHD. 3 hits. [Graphical view]
SUPFAM	SSF46774. ARID. 1 hit. SSF57903. FYVE_PHD_ZnF. 3 hits.
PROSITE	PS51011. 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]
ProtoNet	Search...
Other
NextBio	785524.

Entry information

Entry name

KDM5_DROME

Accession

Primary (citable) accession number: Q9VMJ7

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 26, 2007
Last sequence update:	May 1, 2000
Last modified:	January 25, 2012
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project