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Protein

Lysine-specific demethylase 7 homolog

Gene

jmjd-1.2

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

Functioni

Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.3 Publications

Cofactori

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per subunit.1 Publication

Enzyme regulationi

Competitively inhibited by 2-hydroxyglutarate.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi508 – 5081Iron; catalyticPROSITE-ProRule annotation2 Publications
Metal bindingi510 – 5101Iron; catalyticPROSITE-ProRule annotation2 Publications
Binding sitei518 – 5181Substrate1 Publication
Binding sitei525 – 5251Substrate1 Publication
Metal bindingi580 – 5801Iron; catalyticPROSITE-ProRule annotation2 Publications
Binding sitei580 – 5801Substrate1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri208 – 29083PHD-typeAdd
BLAST

GO - Molecular functioni

  • dioxygenase activity Source: UniProtKB-KW
  • histone binding Source: WormBase
  • histone demethylase activity (H3-K27 specific) Source: WormBase
  • histone demethylase activity (H3-K9 specific) Source: WormBase
  • zinc ion binding Source: InterPro

GO - Biological processi

  • histone H3-K27 demethylation Source: WormBase
  • histone H3-K9 demethylation Source: WormBase
  • regulation of locomotion Source: WormBase
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-CEL-3214842. HDMs demethylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 7 homolog (EC:1.14.11.-)
Short name:
ceKDM7A
Alternative name(s):
JmjC domain-containing protein 1.2
PHD finger protein 8 homolog
PHF8 homolog
Gene namesi
Name:jmjd-1.2
ORF Names:F29B9.2
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome IV

Organism-specific databases

WormBaseiF29B9.2a; CE09781; WBGene00017920; jmjd-1.2.
F29B9.2b; CE27145; WBGene00017920; jmjd-1.2.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Impaired locomotion. While wild-type animals move by alternating dorsal and ventral flexions along the body length, producing a regular sinusoidal track on bacteria, the track pattern left mutants is irregular, with increased wavelength (distance between successive peaks of a wave) but unchanged amplitude of the wave. An increase of H3K9me2 and H3K27me2 levels is observed.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi209 – 2091D → A: Abolishes binding to H3K4me3. 1 Publication
Mutagenesisi254 – 2541W → A: Abolishes binding to H3K4me3. 1 Publication
Mutagenesisi258 – 2581D → A: Abolishes binding to H3K4me3. 1 Publication
Mutagenesisi261 – 2611Q → A: Abolishes binding to H3K4me3. 1 Publication
Mutagenesisi263 – 2631W → A: Abolishes binding to H3K4me3. 1 Publication
Mutagenesisi402 – 4021D → A: Impairs histone methyltransferase activity. 1 Publication
Mutagenesisi409 – 4091Q → A: Impairs histone methyltransferase activity. 1 Publication
Mutagenesisi411 – 4111T → A: Impairs histone methyltransferase activity. 1 Publication
Mutagenesisi437 – 4371S → A: Abolishes histone methyltransferase activity. 1 Publication
Mutagenesisi495 – 4951F → A: Strongly impairs histone methyltransferase activity. 1 Publication
Mutagenesisi510 – 5101D → A: Strongly impairs histone methyltransferase activity. 1 Publication
Mutagenesisi518 – 5181Y → A: Strongly impairs histone methyltransferase activity. 1 Publication
Mutagenesisi544 – 5441E → A: Impairs histone methyltransferase activity. 1 Publication
Mutagenesisi594 – 5941N → A: Strongly impairs histone methyltransferase activity. 1 Publication
Mutagenesisi622 – 6243EKF → AAA: Abolishes histone methyltransferase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 910910Lysine-specific demethylase 7 homologPRO_0000399813Add
BLAST

Proteomic databases

EPDiQ9GYI0.
PaxDbiQ9GYI0.
PRIDEiQ9GYI0.

Expressioni

Tissue specificityi

Mainly expressed in neurons. Also weakly expressed in some muscle, intestinal and hypodermal cells.1 Publication

Gene expression databases

ExpressionAtlasiQ9GYI0. baseline and differential.

Interactioni

GO - Molecular functioni

  • histone binding Source: WormBase

Protein-protein interaction databases

IntActiQ9GYI0. 2 interactions.
STRINGi6239.F29B9.2a.

Structurei

Secondary structure

1
910
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi207 – 2093Combined sources
Turni212 – 2143Combined sources
Turni244 – 2496Combined sources
Beta strandi253 – 2564Combined sources
Turni258 – 2603Combined sources
Beta strandi263 – 2653Combined sources
Helixi266 – 2683Combined sources
Helixi273 – 2753Combined sources
Turni276 – 2783Combined sources
Beta strandi279 – 2813Combined sources
Turni285 – 2873Combined sources
Helixi288 – 2914Combined sources
Beta strandi304 – 3063Combined sources
Helixi310 – 3123Combined sources
Helixi322 – 33110Combined sources
Helixi332 – 3343Combined sources
Turni340 – 3423Combined sources
Beta strandi343 – 3486Combined sources
Helixi349 – 35810Combined sources
Helixi362 – 3643Combined sources
Beta strandi367 – 3737Combined sources
Helixi388 – 3958Combined sources
Beta strandi400 – 4056Combined sources
Turni406 – 4094Combined sources
Beta strandi410 – 4156Combined sources
Helixi416 – 4249Combined sources
Beta strandi433 – 4353Combined sources
Helixi446 – 4494Combined sources
Helixi454 – 4596Combined sources
Helixi461 – 4655Combined sources
Helixi474 – 4785Combined sources
Beta strandi479 – 4813Combined sources
Helixi486 – 4883Combined sources
Beta strandi493 – 4997Combined sources
Beta strandi503 – 5086Combined sources
Helixi511 – 5133Combined sources
Beta strandi515 – 53016Combined sources
Helixi534 – 54512Combined sources
Helixi553 – 5564Combined sources
Turni557 – 5593Combined sources
Beta strandi562 – 5676Combined sources
Beta strandi571 – 5744Combined sources
Beta strandi579 – 59517Combined sources
Helixi598 – 6003Combined sources
Helixi601 – 61717Combined sources
Helixi622 – 6243Combined sources
Helixi629 – 63911Combined sources
Helixi641 – 65010Combined sources
Helixi656 – 68328Combined sources
Helixi693 – 71523Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N9LX-ray2.80A201-724[»]
3N9MX-ray2.49A/C201-724[»]
3N9NX-ray2.30A201-724[»]
3N9OX-ray2.31A201-724[»]
3N9PX-ray2.39A201-724[»]
3N9QX-ray2.30A201-724[»]
3PUQX-ray2.25A/C201-724[»]
3PURX-ray2.10A/C201-724[»]
ProteinModelPortaliQ9GYI0.
SMRiQ9GYI0. Positions 206-719.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9GYI0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini441 – 612172JmjCPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni505 – 5106Substrate binding

Domaini

The PHD-type zinc finger mediates binding to H3K4me3.2 Publications

Sequence similaritiesi

Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 PHD-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri208 – 29083PHD-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1633. Eukaryota.
ENOG410XQXU. LUCA.
GeneTreeiENSGT00550000074396.
HOGENOMiHOG000016428.
InParanoidiQ9GYI0.
OMAiCTSSGRK.
OrthoDBiEOG73JKV9.
PhylomeDBiQ9GYI0.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform a (identifier: Q9GYI0-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MDGNDINIQK NEFSRDQSAL LMMDQHSDHK NHESAIGEPG MSYTASQPAL
60 70 80 90 100
SSTEHQTPLV SEASVAAPQN HLNGNSHESV SEMDRNSVDF AIESVLMKAR
110 120 130 140 150
AYNKMGAPKD PRRKQHNPKS EPKIEPHVTD SSDNQAAMSN KMEAEAPKME
160 170 180 190 200
SNQNYVSNGS EPPFRFVSIS NFDEMKTKKK EVQEELKLEV DSDSEEDDVP
210 220 230 240 250
EQKTPKESDR CGGCGKFTHE DDLIALEEEK KKEKEKPLMS KKKSHHHKKN
260 270 280 290 300
DFQWIGCDSC QTWYHFLCSG LEQFEYYLYE KFFCPKCVPH TGHSIRYKVV
310 320 330 340 350
APHRYRWYSP NEKHLGIEVG SKTWIEDFIT RENTVPSPTD DEVCIVEDGY
360 370 380 390 400
EFRREFEKLG GADNWGKVFM VKDMDGLNMT MPKPGFDLED VVKIMGSDYE
410 420 430 440 450
VDTIDVYNQS TYSMKLDTFR KLFRDTKNRP LLYNFLSLEF SDNNEMKEIA
460 470 480 490 500
KPPRFVQEIS MVNRLWPDVS GAEYIKLLQR EEYLPEDQRP KVEQFCLAGM
510 520 530 540 550
AGSYTDFHVD FGGSSVYYHI LKGEKIFYIA APTEQNFAAY QAHETSPDTT
560 570 580 590 600
TWFGDIANGA VKRVVIKEGQ TLLIPAGWIH AVLTPVDSLV FGGNFLHLGN
610 620 630 640 650
LEMQMRVYHL ENAIRKEIRS EEKFYFPNFE LLHWMYMRNV LLEKITEANQ
660 670 680 690 700
EGSDMREQEK NIWTASQIMK AEMERWMDRE LRLGPEKNAI LPTDDKNKIM
710 720 730 740 750
ISVRKQIEIQ TKIQNAKNKP MGLKQKRKSR ESAERDDEDY CPSSSTAYKK
760 770 780 790 800
KYTKKAKKDN DDAPKVKKAK KEEVPEEKVP VPEAAGPSEV TAPLTIKIGM
810 820 830 840 850
GPTEDQKGVV QIFNNQCTSS GRKVKLNQNV ADYCGSHLEA RVEEIPEKAT
860 870 880 890 900
KSFRELDNEL ERCEAVHSGE KIKKVKEPKP PKQPKEKKEK PPPKKKEMSS
910
RDRLMKKLKM
Length:910
Mass (Da):104,672
Last modified:March 1, 2001 - v1
Checksum:i8AE17DC5860EDFA5
GO
Isoform b (identifier: Q9GYI0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     86-98: Missing.

Note: No experimental confirmation available.
Show »
Length:897
Mass (Da):103,238
Checksum:i9D762C5F14FB0F41
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei86 – 9813Missing in isoform b. CuratedVSP_039912Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO081255 Genomic DNA. Translation: CCD70224.1.
FO081255 Genomic DNA. Translation: CCD70225.1.
PIRiT29935.
RefSeqiNP_500610.1. NM_068209.4. [Q9GYI0-1]
NP_500611.1. NM_068210.3. [Q9GYI0-2]
UniGeneiCel.17181.

Genome annotation databases

EnsemblMetazoaiF29B9.2a; F29B9.2a; WBGene00017920. [Q9GYI0-1]
GeneIDi177232.
UCSCiF29B9.2a. c. elegans. [Q9GYI0-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO081255 Genomic DNA. Translation: CCD70224.1.
FO081255 Genomic DNA. Translation: CCD70225.1.
PIRiT29935.
RefSeqiNP_500610.1. NM_068209.4. [Q9GYI0-1]
NP_500611.1. NM_068210.3. [Q9GYI0-2]
UniGeneiCel.17181.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N9LX-ray2.80A201-724[»]
3N9MX-ray2.49A/C201-724[»]
3N9NX-ray2.30A201-724[»]
3N9OX-ray2.31A201-724[»]
3N9PX-ray2.39A201-724[»]
3N9QX-ray2.30A201-724[»]
3PUQX-ray2.25A/C201-724[»]
3PURX-ray2.10A/C201-724[»]
ProteinModelPortaliQ9GYI0.
SMRiQ9GYI0. Positions 206-719.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9GYI0. 2 interactions.
STRINGi6239.F29B9.2a.

Proteomic databases

EPDiQ9GYI0.
PaxDbiQ9GYI0.
PRIDEiQ9GYI0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiF29B9.2a; F29B9.2a; WBGene00017920. [Q9GYI0-1]
GeneIDi177232.
UCSCiF29B9.2a. c. elegans. [Q9GYI0-1]

Organism-specific databases

CTDi177232.
WormBaseiF29B9.2a; CE09781; WBGene00017920; jmjd-1.2.
F29B9.2b; CE27145; WBGene00017920; jmjd-1.2.

Phylogenomic databases

eggNOGiKOG1633. Eukaryota.
ENOG410XQXU. LUCA.
GeneTreeiENSGT00550000074396.
HOGENOMiHOG000016428.
InParanoidiQ9GYI0.
OMAiCTSSGRK.
OrthoDBiEOG73JKV9.
PhylomeDBiQ9GYI0.

Enzyme and pathway databases

ReactomeiR-CEL-3214842. HDMs demethylate histones.

Miscellaneous databases

EvolutionaryTraceiQ9GYI0.
NextBioi895906.
PROiQ9GYI0.

Gene expression databases

ExpressionAtlasiQ9GYI0. baseline and differential.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  2. "Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans."
    Lin H., Wang Y., Wang Y., Tian F., Pu P., Yu Y., Mao H., Yang Y., Wang P., Hu L., Lin Y., Liu Y., Xu Y., Chen C.D.
    Cell Res. 20:899-907(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN PHD-FINGER.
  3. "A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation."
    Kleine-Kohlbrecher D., Christensen J., Vandamme J., Abarrategui I., Bak M., Tommerup N., Shi X., Gozani O., Rappsilber J., Salcini A.E., Helin K.
    Mol. Cell 38:165-178(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  4. "Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans."
    Yang Y., Hu L., Wang P., Hou H., Lin Y., Liu Y., Li Z., Gong R., Feng X., Zhou L., Zhang W., Dong Y., Yang H., Lin H., Wang Y., Chen C.D., Xu Y.
    Cell Res. 20:886-898(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 205-719 IN COMPLEX WITH ZINC; IRON AND METHYLATED H3 PEPTIDES, ZINC-BINDING, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN PHD-FINGER, MUTAGENESIS OF ASP-209; TRP-254; ASP-258; GLN-261; TRP-263; ASP-402; GLN-409; THR-411; SER-437; PHE-495; ASP-510; TYR-518; GLU-544; ASN-594 AND 622-GLU--PHE-624.
  5. "Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases."
    Xu W., Yang H., Liu Y., Yang Y., Wang P., Kim S.H., Ito S., Yang C., Wang P., Xiao M.T., Liu L.X., Jiang W.Q., Liu J., Zhang J.Y., Wang B., Frye S., Zhang Y., Xu Y.H.
    , Lei Q.Y., Guan K.L., Zhao S.M., Xiong Y.
    Cancer Cell 19:17-30(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 201-724 IN COMPLEX WITH SUBSTRATE; INHIBITOR; IRON AND ZINC, ENZYME REGULATION.

Entry informationi

Entry nameiKDM7_CAEEL
AccessioniPrimary (citable) accession number: Q9GYI0
Secondary accession number(s): Q9BI67
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 5, 2010
Last sequence update: March 1, 2001
Last modified: March 16, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  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.