JmjC domain-containing histone demethylation protein 1A

Names and origin

Protein names

Recommended name:
    JmjC domain-containing histone demethylation protein 1A
    EC=1.14.11.27
Alternative name(s):
    [Histone-H3]-lysine-36 demethylase 1A
    F-box/LRR-repeat protein 11
    F-box and leucine-rich repeat protein 11
    F-box protein FBL7
    F-box protein Lilina
    CXXC-type zinc finger protein 8

Gene names

Name:	FBXL11
Synonyms:	CXXC8, FBL7, JHDM1A, KIAA1004

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	1162 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylted H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promotes their ubiquitination and degradation.
Catalytic activity	Protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2). Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate + formaldehyde + CO(2).
Cofactor	Binds 1 Fe(2+) ion per subunit.
Subunit structure	Part of a SCF (SKP1-cullin-F-box) protein ligase complex By similarity.
Subcellular location	NucleusProbable.
Tissue specificity	Widely expressed, with highest levels in brain, testis and ovary, followed by lung.
Domain	The JmjC domain mediates the demethylation activity.
Post-translational modification	Phosphorylated upon DNA damage, probably by ATM or ATR.
Sequence similarities	Belongs to the JHDM1 histone demethylase family. Contains 1 CXXC-type zinc finger. Contains 1 F-box domain. Contains 1 JmjC domain. Contains 3 LRR (leucine-rich) repeats. Contains 1 PHD-type zinc finger.
Sequence caution	The sequence BAB15795.1 differs from that shown. Reason: Frameshift at position 410.

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Ontologies

Keywords
Biological process	Transcription Transcription regulation Ubl conjugation pathway
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Leucine-rich repeat Repeat Zinc-finger
Ligand	Iron Metal-binding Zinc
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase
PTM	Phosphoprotein
Gene Ontology (GO)
Molecular function	protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
SKP1	P63208	1	EBI-765758,EBI-307486

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Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9Y2K7-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q9Y2K7-2) The sequence of this isoform differs from the canonical sequence as follows: 1-306: Missing.
Notes: No experimental confirmation available.

Isoform 3 (identifier: Q9Y2K7-3) The sequence of this isoform differs from the canonical sequence as follows: 774-782: REKENNPSG → LRQETLDKN 783-1162: Missing.
Notes: No experimental confirmation available.

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1162

1162

JmjC domain-containing histone demethylation protein 1A

PRO_0000119855

Regions

Domain

148 – 316

169

JmjC

Domain

889 – 936

48

F-box

Repeat

1000 – 1025

26

LRR 1

Repeat

1063 – 1091

29

LRR 2

Repeat

1095 – 1118

24

LRR 3

Zinc finger

564 – 610

47

CXXC-type

Zinc finger

617 – 678

62

PHD-type

Sites

Metal binding

212

1

Iron; catalytic Probable

Metal binding

214

1

Iron; catalytic By similarity

Metal binding

284

1

Iron; catalytic By similarity

Binding site

209

1

Substrate By similarity

Binding site

229

1

Substrate By similarity

Amino acid modifications

Modified residue

28

1

Phosphoserine

Modified residue

534

1

Phosphothreonine

Modified residue

550

1

Phosphothreonine

Modified residue

558

1

Phosphoserine

Modified residue

632

1

Phosphothreonine

Modified residue

713

1

Phosphothreonine

Modified residue

718

1

Phosphoserine

Modified residue

720

1

Phosphothreonine

Modified residue

731

1

Phosphoserine

Modified residue

739

1

Phosphoserine

Modified residue

740

1

Phosphoserine

Natural variations

Alternative sequence

1 – 306

306

Missing in isoform 2.

VSP_017468

Alternative sequence

774 – 782

9

REKENNPSG → LRQETLDKN in isoform 3.

VSP_017469

Alternative sequence

783 – 1162

380

Missing in isoform 3.

VSP_017470

Experimental info

Mutagenesis

212

1

H → A: Abolishes histone demethylase activity

Sequence conflict

518

1

K → I in AAH47371. Ref.5

Sequence conflict

657

1

D → G in AAH47371. Ref.5

Sequence conflict

1128

1

Missing in AAH01203. Ref.5

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Sequences

Sequence		Length	Mass (Da)
Isoform 1 [UniParc]. Last modified November 7, 2003. Version 3. Checksum: 88620A363A5C5842 Show »	FASTA	1,162	132,793
10 20 30 40 50 60 MEPEEERIRY SQRLRGTMRR RYEDDGISDD EIEGKRTFDL EEKLHTNKYN ANFVTFMEGK 70 80 90 100 110 120 DFNVEYIQRG GLRDPLIFKN SDGLGIKMPD PDFTVNDVKM CVGSRRMVDV MDVNTQKGIE 130 140 150 160 170 180 MTMAQWTRYY ETPEEEREKL YNVISLEFSH TRLENMVQRP STVDFIDWVD NMWPRHLKES 190 200 210 220 230 240 QTESTNAILE MQYPKVQKYC LMSVRGCYTD FHVDFGGTSV WYHIHQGGKV FWLIPPTAHN 250 260 270 280 290 300 LELYENWLLS GKQGDIFLGD RVSDCQRIEL KQGYTFVIPS GWIHAVYTPT DTLVFGGNFL 310 320 330 340 350 360 HSFNIPMQLK IYNIEDRTRV PNKFRYPFYY EMCWYVLERY VYCITNRSHL TKEFQKESLS 370 380 390 400 410 420 MDLELNGLES GNGDEEAVDR EPRRLSSRRS VLTSPVANGV NLDYDGLGKT CRSLPSLKKT 430 440 450 460 470 480 LAGDSSSDCS RGSHNGQVWD PQCAPRKDRQ VHLTHFELEG LRCLVDKLES LPLHKKCVPT 490 500 510 520 530 540 GIEDEDALIA DVKILLEELA NSDPKLALTG VPIVQWPKRD KLKFPTRPKV RVPTIPITKP 550 560 570 580 590 600 HTMKPAPRLT PVRPAAASPI VSGARRRRVR CRKCKACVQG ECGVCHYCRD MKKFGGPGRM 610 620 630 640 650 660 KQSCVLRQCL APRLPHSVTC SLCGEVDQNE ETQDFEKKLM ECCICNEIVH PGCLQMDGEG 670 680 690 700 710 720 LLNEELPNCW ECPKCYQEDS SEKAQKRKME ESDEEAVQAK VLRPLRSCDE PLTPPPHSPT 730 740 750 760 770 780 SMLQLIHDPV SPRGMVTRSS PGAGPSDHHS ASRDERFKRR QLLRLQATER TMVREKENNP 790 800 810 820 830 840 SGKKELSEVE KAKIRGSYLT VTLQRPTKEL HGTSIVPKLQ AITASSANLR HSPRVLVQHC 850 860 870 880 890 900 PARTPQRGDE EGLGGEEEEE EEEEEEDDSA EEGGAARLNG RGSWAQDGDE SWMQREVWMS 910 920 930 940 950 960 VFRYLSRREL CECMRVCKTW YKWCCDKRLW TKIDLSRCKA IVPQALSGII KRQPVSLDLS 970 980 990 1000 1010 1020 WTNISKKQLT WLVNRLPGLK DLLLAGCSWS AVSALSTSSC PLLRTLDLRW AVGIKDPQIR 1030 1040 1050 1060 1070 1080 DLLTPPADKP GQDNRSKLRN MTDFRLAGLD ITDATLRLII RHMPLLSRLD LSHCSHLTDQ 1090 1100 1110 1120 1130 1140 SSNLLTAVGS STRYSLTELN MAGCNKLTDQ TLIYLRRIAN VTLIDLRGCK QITRKACEHF 1150 1160 ISDLSINSLY CLSDEKLIQK IS « Hide
Isoform 2 [UniParc]. Checksum: C1351A450B4482E0 Show »		856	96,859
10 20 30 40 50 60 MQLKIYNIED RTRVPNKFRY PFYYEMCWYV LERYVYCITN RSHLTKEFQK ESLSMDLELN 70 80 90 100 110 120 GLESGNGDEE AVDREPRRLS SRRSVLTSPV ANGVNLDYDG LGKTCRSLPS LKKTLAGDSS 130 140 150 160 170 180 SDCSRGSHNG QVWDPQCAPR KDRQVHLTHF ELEGLRCLVD KLESLPLHKK CVPTGIEDED 190 200 210 220 230 240 ALIADVKILL EELANSDPKL ALTGVPIVQW PKRDKLKFPT RPKVRVPTIP ITKPHTMKPA 250 260 270 280 290 300 PRLTPVRPAA ASPIVSGARR RRVRCRKCKA CVQGECGVCH YCRDMKKFGG PGRMKQSCVL 310 320 330 340 350 360 RQCLAPRLPH SVTCSLCGEV DQNEETQDFE KKLMECCICN EIVHPGCLQM DGEGLLNEEL 370 380 390 400 410 420 PNCWECPKCY QEDSSEKAQK RKMEESDEEA VQAKVLRPLR SCDEPLTPPP HSPTSMLQLI 430 440 450 460 470 480 HDPVSPRGMV TRSSPGAGPS DHHSASRDER FKRRQLLRLQ ATERTMVREK ENNPSGKKEL 490 500 510 520 530 540 SEVEKAKIRG SYLTVTLQRP TKELHGTSIV PKLQAITASS ANLRHSPRVL VQHCPARTPQ 550 560 570 580 590 600 RGDEEGLGGE EEEEEEEEEE DDSAEEGGAA RLNGRGSWAQ DGDESWMQRE VWMSVFRYLS 610 620 630 640 650 660 RRELCECMRV CKTWYKWCCD KRLWTKIDLS RCKAIVPQAL SGIIKRQPVS LDLSWTNISK 670 680 690 700 710 720 KQLTWLVNRL PGLKDLLLAG CSWSAVSALS TSSCPLLRTL DLRWAVGIKD PQIRDLLTPP 730 740 750 760 770 780 ADKPGQDNRS KLRNMTDFRL AGLDITDATL RLIIRHMPLL SRLDLSHCSH LTDQSSNLLT 790 800 810 820 830 840 AVGSSTRYSL TELNMAGCNK LTDQTLIYLR RIANVTLIDL RGCKQITRKA CEHFISDLSI 850 NSLYCLSDEK LIQKIS « Hide
Isoform 3 [UniParc]. Checksum: 667E9A3E503C6550 Show »		782	89,948
10 20 30 40 50 60 MEPEEERIRY SQRLRGTMRR RYEDDGISDD EIEGKRTFDL EEKLHTNKYN ANFVTFMEGK 70 80 90 100 110 120 DFNVEYIQRG GLRDPLIFKN SDGLGIKMPD PDFTVNDVKM CVGSRRMVDV MDVNTQKGIE 130 140 150 160 170 180 MTMAQWTRYY ETPEEEREKL YNVISLEFSH TRLENMVQRP STVDFIDWVD NMWPRHLKES 190 200 210 220 230 240 QTESTNAILE MQYPKVQKYC LMSVRGCYTD FHVDFGGTSV WYHIHQGGKV FWLIPPTAHN 250 260 270 280 290 300 LELYENWLLS GKQGDIFLGD RVSDCQRIEL KQGYTFVIPS GWIHAVYTPT DTLVFGGNFL 310 320 330 340 350 360 HSFNIPMQLK IYNIEDRTRV PNKFRYPFYY EMCWYVLERY VYCITNRSHL TKEFQKESLS 370 380 390 400 410 420 MDLELNGLES GNGDEEAVDR EPRRLSSRRS VLTSPVANGV NLDYDGLGKT CRSLPSLKKT 430 440 450 460 470 480 LAGDSSSDCS RGSHNGQVWD PQCAPRKDRQ VHLTHFELEG LRCLVDKLES LPLHKKCVPT 490 500 510 520 530 540 GIEDEDALIA DVKILLEELA NSDPKLALTG VPIVQWPKRD KLKFPTRPKV RVPTIPITKP 550 560 570 580 590 600 HTMKPAPRLT PVRPAAASPI VSGARRRRVR CRKCKACVQG ECGVCHYCRD MKKFGGPGRM 610 620 630 640 650 660 KQSCVLRQCL APRLPHSVTC SLCGEVDQNE ETQDFEKKLM ECCICNEIVH PGCLQMDGEG 670 680 690 700 710 720 LLNEELPNCW ECPKCYQEDS SEKAQKRKME ESDEEAVQAK VLRPLRSCDE PLTPPPHSPT 730 740 750 760 770 780 SMLQLIHDPV SPRGMVTRSS PGAGPSDHHS ASRDERFKRR QLLRLQATER TMVLRQETLD KN « Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"cDNA cloning and expression analysis of new members of the mammalian F-box protein family." Ilyin G.P., Rialland M., Pigeon C., Guguen-Guillouzo C. Genomics 67:40-47(2000) [PubMed: 10945468] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]	"Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro." Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 6:63-70(1999) [PubMed: 10231032] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), TISSUE SPECIFICITY. Tissue: Brain.
[3]	"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones." Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T. DNA Res. 9:99-106(2002) [PubMed: 12168954] [Abstract] Cited for: SEQUENCE REVISION.
[4]	"Characterization of long cDNA clones from human adult spleen." Hattori A., Okumura K., Nagase T., Kikuno R., Hirosawa M., Ohara O. DNA Res. 7:357-366(2000) [PubMed: 11214971] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Spleen.
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3). Tissue: Eye, Testis and Uterus.
[6]	Pagano M. Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 667-1162.
[7]	The German cDNA consortium Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1134-1162. Tissue: Testis.
[8]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-28, MASS SPECTROMETRY. Tissue: Epithelium.
[9]	"Histone demethylation by a family of JmjC domain-containing proteins." Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., Zhang Y. Nature 439:811-816(2006) [PubMed: 16362057] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN, MUTAGENESIS OF HIS-212.
[10]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-534, MASS SPECTROMETRY. Tissue: Epithelium.
[11]	"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage." Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J. Science 316:1160-1166(2007) [PubMed: 17525332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-632, MASS SPECTROMETRY.
[12]	"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis." Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III J. Proteome Res. 7:1346-1351(2008) [PubMed: 18220336] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-550; SER-558; THR-713; SER-718; THR-720; SER-731; SER-739 AND SER-740, MASS SPECTROMETRY.

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Cross-references

Sequence databases
	AB023221 mRNA. Translation: BAA76848.2. Different initiation. AK024505 mRNA. Translation: BAB15795.1. Frameshift. BC001203 mRNA. Translation: AAH01203.1. BC047371 mRNA. Translation: AAH47371.1. BC047486 mRNA. Translation: AAH47486.1. BC064360 mRNA. Translation: AAH64360.1. AF179221 mRNA. Translation: AAD56012.1. Different initiation. AL117517 mRNA. Translation: CAH10721.1.
RefSeq	NP_036440.1.
UniGene	Hs.124147
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9Y2K7.
PTM databases
PhosphoSite	Q9Y2K7.
Genome annotation databases
Ensembl	ENSG00000173120. Homo sapiens. [Contig view]
GeneID	22992.
KEGG	hsa:22992.
Organism-specific databases
H-InvDB	HIX0023005.
HGNC	HGNC:13606. FBXL11.
HPA	CAB012272.
MIM	605657. gene.
PharmGKB	PA28020.
HUGE	Search...
GenAtlas	Search...
GeneCards	Search...
Phylogenomic databases
HOVERGEN	Q9Y2K7.
Gene expression databases
ArrayExpress	Q9Y2K7.
CleanEx	HS_FBXL11.
Family and domain databases
InterPro	IPR001810. F-box. IPR001611. LRR. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR002857. Znf_CXXC. IPR001965. Znf_PHD. [Graphical view]
Pfam	PF00646. F-box. 1 hit. PF02373. JmjC. 1 hit. PF00560. LRR_1. 1 hit. PF02008. zf-CXXC. 1 hit. [Graphical view]
SMART	SM00256. FBOX. 1 hit. SM00558. JmjC. 1 hit. SM00249. PHD. 1 hit. [Graphical view]
PROSITE	PS50181. FBOX. False negative. PS51184. JMJC. 1 hit. PS51058. ZF_CXXC. 1 hit. PS01359. ZF_PHD_1. 1 hit. PS50016. ZF_PHD_2. 1 hit. [Graphical view]
BLOCKS	Search...
ProtoNet	Search...
Other Resources
NextBio	43847.
SOURCE	Search...

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Entry information

Entry name

JHD1A_HUMAN

Accession

Primary (citable) accession number: Q9Y2K7
Secondary accession number(s): Q49A21

Q9UK66

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 7, 2003
Last sequence update:	November 7, 2003
Last modified:	November 4, 2008
This is version 67 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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Relevant documents

Human chromosome 11

Human chromosome 11: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

UniProtKB secondary accession numbers

Index of UniProtKB secondary accession numbers

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Keywords

Gene Ontology (GO)

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Natural variations

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents