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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)DescriptionActionsGraphical viewLength
Metal bindingi508Iron; catalyticPROSITE-ProRule annotation2 Publications1
Metal bindingi510Iron; catalyticPROSITE-ProRule annotation2 Publications1
Binding sitei518Substrate1 Publication1
Binding sitei525Substrate1 Publication1
Metal bindingi580Iron; catalyticPROSITE-ProRule annotation2 Publications1
Binding sitei580Substrate1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri208 – 290PHD-typeAdd BLAST83

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-2299718. Condensation of Prophase Chromosomes.
R-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
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)DescriptionActionsGraphical viewLength
Mutagenesisi209D → A: Abolishes binding to H3K4me3. 1 Publication1
Mutagenesisi254W → A: Abolishes binding to H3K4me3. 1 Publication1
Mutagenesisi258D → A: Abolishes binding to H3K4me3. 1 Publication1
Mutagenesisi261Q → A: Abolishes binding to H3K4me3. 1 Publication1
Mutagenesisi263W → A: Abolishes binding to H3K4me3. 1 Publication1
Mutagenesisi402D → A: Impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi409Q → A: Impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi411T → A: Impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi437S → A: Abolishes histone methyltransferase activity. 1 Publication1
Mutagenesisi495F → A: Strongly impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi510D → A: Strongly impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi518Y → A: Strongly impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi544E → A: Impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi594N → A: Strongly impairs histone methyltransferase activity. 1 Publication1
Mutagenesisi622 – 624EKF → AAA: Abolishes histone methyltransferase activity. 1 Publication3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003998131 – 910Lysine-specific demethylase 7 homologAdd BLAST910

Proteomic databases

EPDiQ9GYI0.
PaxDbiQ9GYI0.
PeptideAtlasiQ9GYI0.
PRIDEiQ9GYI0.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiWBGene00017920.
ExpressionAtlasiQ9GYI0. differential.

Interactioni

GO - Molecular functioni

  • histone binding Source: WormBase

Protein-protein interaction databases

IntActiQ9GYI0. 2 interactors.
STRINGi6239.F29B9.2a.

Structurei

Secondary structure

1910
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi207 – 209Combined sources3
Turni212 – 214Combined sources3
Turni244 – 249Combined sources6
Beta strandi253 – 256Combined sources4
Turni258 – 260Combined sources3
Beta strandi263 – 265Combined sources3
Helixi266 – 268Combined sources3
Helixi273 – 275Combined sources3
Turni276 – 278Combined sources3
Beta strandi279 – 281Combined sources3
Turni285 – 287Combined sources3
Helixi288 – 291Combined sources4
Beta strandi304 – 306Combined sources3
Helixi310 – 312Combined sources3
Helixi322 – 331Combined sources10
Helixi332 – 334Combined sources3
Turni340 – 342Combined sources3
Beta strandi343 – 348Combined sources6
Helixi349 – 358Combined sources10
Helixi362 – 364Combined sources3
Beta strandi367 – 373Combined sources7
Helixi388 – 395Combined sources8
Beta strandi400 – 405Combined sources6
Turni406 – 409Combined sources4
Beta strandi410 – 415Combined sources6
Helixi416 – 424Combined sources9
Beta strandi433 – 435Combined sources3
Helixi446 – 449Combined sources4
Helixi454 – 459Combined sources6
Helixi461 – 465Combined sources5
Helixi474 – 478Combined sources5
Beta strandi479 – 481Combined sources3
Helixi486 – 488Combined sources3
Beta strandi493 – 499Combined sources7
Beta strandi503 – 508Combined sources6
Helixi511 – 513Combined sources3
Beta strandi515 – 530Combined sources16
Helixi534 – 545Combined sources12
Helixi553 – 556Combined sources4
Turni557 – 559Combined sources3
Beta strandi562 – 567Combined sources6
Beta strandi571 – 574Combined sources4
Beta strandi579 – 595Combined sources17
Helixi598 – 600Combined sources3
Helixi601 – 617Combined sources17
Helixi622 – 624Combined sources3
Helixi629 – 639Combined sources11
Helixi641 – 650Combined sources10
Helixi656 – 683Combined sources28
Helixi693 – 715Combined sources23

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9GYI0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini441 – 612JmjCPROSITE-ProRule annotationAdd BLAST172

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni505 – 510Substrate binding6

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)DescriptionActionsGraphical viewLength
Zinc fingeri208 – 290PHD-typeAdd BLAST83

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1633. Eukaryota.
ENOG410XQXU. LUCA.
GeneTreeiENSGT00550000074396.
HOGENOMiHOG000016428.
InParanoidiQ9GYI0.
OMAiCTSSGRK.
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)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_03991286 – 98Missing in isoform b. CuratedAdd BLAST13

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.

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9GYI0. 2 interactors.
STRINGi6239.F29B9.2a.

Proteomic databases

EPDiQ9GYI0.
PaxDbiQ9GYI0.
PeptideAtlasiQ9GYI0.
PRIDEiQ9GYI0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

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.
PhylomeDBiQ9GYI0.

Enzyme and pathway databases

ReactomeiR-CEL-2299718. Condensation of Prophase Chromosomes.
R-CEL-3214842. HDMs demethylate histones.

Miscellaneous databases

EvolutionaryTraceiQ9GYI0.
PROiQ9GYI0.

Gene expression databases

BgeeiWBGene00017920.
ExpressionAtlasiQ9GYI0. 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...

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: November 30, 2016
This is version 115 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.