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Lysine-specific demethylase 7 homolog (ceKDM7A) (EC 1.14.11.-) (JmjC domain-containing protein 1.2) (PHD finger protein 8 homolog) (PHF8 homolog)

 KDM7_CAEEL              Reviewed;         910 AA.
Q9GYI0; Q9BI67;
05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
25-OCT-2017, entry version 123.
RecName: Full=Lysine-specific demethylase 7 homolog;
Short=ceKDM7A;
EC=1.14.11.-;
AltName: Full=JmjC domain-containing protein 1.2;
AltName: Full=PHD finger protein 8 homolog;
AltName: Full=PHF8 homolog;
Name=jmjd-1.2; ORFNames=F29B9.2;
Caenorhabditis elegans.
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
NCBI_TaxID=6239;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Bristol N2;
PubMed=9851916; DOI=10.1126/science.282.5396.2012;
The C. elegans sequencing consortium;
"Genome sequence of the nematode C. elegans: a platform for
investigating biology.";
Science 282:2012-2018(1998).
[2]
FUNCTION, AND DOMAIN PHD-FINGER.
PubMed=20567262; DOI=10.1038/cr.2010.84;
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.;
"Coordinated regulation of active and repressive histone methylations
by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis
elegans.";
Cell Res. 20:899-907(2010).
[3]
FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND TISSUE
SPECIFICITY.
PubMed=20346720; DOI=10.1016/j.molcel.2010.03.002;
Kleine-Kohlbrecher D., Christensen J., Vandamme J., Abarrategui I.,
Bak M., Tommerup N., Shi X., Gozani O., Rappsilber J., Salcini A.E.,
Helin K.;
"A functional link between the histone demethylase PHF8 and the
transcription factor ZNF711 in X-linked mental retardation.";
Mol. Cell 38:165-178(2010).
[4]
FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF HIS-508.
PubMed=27133168; DOI=10.1016/j.cell.2016.04.012;
Merkwirth C., Jovaisaite V., Durieux J., Matilainen O., Jordan S.D.,
Quiros P.M., Steffen K.K., Williams E.G., Mouchiroud L., Tronnes S.U.,
Murillo V., Wolff S.C., Shaw R.J., Auwerx J., Dillin A.;
"Two Conserved Histone Demethylases Regulate Mitochondrial Stress-
Induced Longevity.";
Cell 165:1209-1223(2016).
[5]
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, AND 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.
PubMed=20567261; DOI=10.1038/cr.2010.86;
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.;
"Structural insights into a dual-specificity histone demethylase
ceKDM7A from Caenorhabditis elegans.";
Cell Res. 20:886-898(2010).
[6]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 201-724 IN COMPLEX WITH
SUBSTRATE; INHIBITOR; IRON AND ZINC, AND ENZYME REGULATION.
PubMed=21251613; DOI=10.1016/j.ccr.2010.12.014;
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.;
"Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of
alpha-ketoglutarate-dependent dioxygenases.";
Cancer Cell 19:17-30(2011).
-!- FUNCTION: Histone demethylase required for nervous system
development (PubMed:20346720). Specifically demethylates
dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2,
respectively) of histone H3, thereby playing a central role in
histone code (PubMed:20346720, PubMed:21251613, PubMed:20567262).
Promotes mitochondrial stress-induced longevity (PubMed:27133168).
{ECO:0000269|PubMed:20346720, ECO:0000269|PubMed:20567261,
ECO:0000269|PubMed:20567262}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
Evidence={ECO:0000269|PubMed:20567261};
Note=Binds 1 Fe(2+) ion per subunit.
{ECO:0000269|PubMed:20567261};
-!- ENZYME REGULATION: Competitively inhibited by 2-hydroxyglutarate.
{ECO:0000269|PubMed:21251613}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20346720}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=a;
IsoId=Q9GYI0-1; Sequence=Displayed;
Name=b;
IsoId=Q9GYI0-2; Sequence=VSP_039912;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Mainly expressed in neurons. Also weakly
expressed in some muscle, intestinal and hypodermal cells.
{ECO:0000269|PubMed:20346720}.
-!- DOMAIN: The PHD-type zinc finger mediates binding to H3K4me3.
{ECO:0000269|PubMed:20567261, ECO:0000269|PubMed:20567262}.
-!- DISRUPTION PHENOTYPE: Impaired locomotion (PubMed:20346720). 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 by mutants is irregular, with
increased wavelength (distance between successive peaks of a wave)
but unchanged amplitude of the wave (PubMed:20346720). An increase
of H3K9me2 and H3K27me2 levels is observed (PubMed:20346720).
RNAi-mediated knockdown suppresses mitochondrial stress-mediated
longevity (PubMed:27133168). {ECO:0000269|PubMed:20346720,
ECO:0000269|PubMed:27133168}.
-!- SIMILARITY: Belongs to the JHDM1 histone demethylase family.
JHDM1D subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; FO081255; CCD70224.1; -; Genomic_DNA.
EMBL; FO081255; CCD70225.1; -; Genomic_DNA.
PIR; T29935; T29935.
RefSeq; NP_500610.1; NM_068209.4. [Q9GYI0-1]
RefSeq; NP_500611.1; NM_068210.3. [Q9GYI0-2]
UniGene; Cel.17181; -.
PDB; 3N9L; X-ray; 2.80 A; A=201-724.
PDB; 3N9M; X-ray; 2.49 A; A/C=201-724.
PDB; 3N9N; X-ray; 2.30 A; A=201-724.
PDB; 3N9O; X-ray; 2.31 A; A=201-724.
PDB; 3N9P; X-ray; 2.39 A; A=201-724.
PDB; 3N9Q; X-ray; 2.30 A; A=201-724.
PDB; 3PUQ; X-ray; 2.25 A; A/C=201-724.
PDB; 3PUR; X-ray; 2.10 A; A/C=201-724.
PDBsum; 3N9L; -.
PDBsum; 3N9M; -.
PDBsum; 3N9N; -.
PDBsum; 3N9O; -.
PDBsum; 3N9P; -.
PDBsum; 3N9Q; -.
PDBsum; 3PUQ; -.
PDBsum; 3PUR; -.
ProteinModelPortal; Q9GYI0; -.
SMR; Q9GYI0; -.
IntAct; Q9GYI0; 2.
STRING; 6239.F29B9.2a; -.
EPD; Q9GYI0; -.
PaxDb; Q9GYI0; -.
PeptideAtlas; Q9GYI0; -.
PRIDE; Q9GYI0; -.
EnsemblMetazoa; F29B9.2a; F29B9.2a; WBGene00017920. [Q9GYI0-1]
GeneID; 177232; -.
UCSC; F29B9.2a; c. elegans.
CTD; 177232; -.
WormBase; F29B9.2a; CE09781; WBGene00017920; jmjd-1.2. [Q9GYI0-1]
WormBase; F29B9.2b; CE27145; WBGene00017920; jmjd-1.2. [Q9GYI0-2]
eggNOG; KOG1633; Eukaryota.
eggNOG; ENOG410XQXU; LUCA.
GeneTree; ENSGT00550000074396; -.
HOGENOM; HOG000016428; -.
InParanoid; Q9GYI0; -.
PhylomeDB; Q9GYI0; -.
EvolutionaryTrace; Q9GYI0; -.
PRO; PR:Q9GYI0; -.
Proteomes; UP000001940; Chromosome IV.
Bgee; WBGene00017920; -.
ExpressionAtlas; Q9GYI0; baseline and differential.
GO; GO:0005634; C:nucleus; IDA:WormBase.
GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
GO; GO:0042393; F:histone binding; IDA:WormBase.
GO; GO:0071558; F:histone demethylase activity (H3-K27 specific); IDA:WormBase.
GO; GO:0032454; F:histone demethylase activity (H3-K9 specific); IDA:WormBase.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0071557; P:histone H3-K27 demethylation; IDA:WormBase.
GO; GO:0033169; P:histone H3-K9 demethylation; IDA:WormBase.
GO; GO:0040012; P:regulation of locomotion; IMP:WormBase.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR003347; JmjC_dom.
InterPro; IPR019786; Zinc_finger_PHD-type_CS.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF02373; JmjC; 1.
SMART; SM00558; JmjC; 1.
SMART; SM00249; PHD; 1.
SUPFAM; SSF57903; SSF57903; 1.
PROSITE; PS51184; JMJC; 1.
PROSITE; PS01359; ZF_PHD_1; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chromatin regulator;
Complete proteome; Dioxygenase; Iron; Metal-binding; Nucleus;
Oxidoreductase; Reference proteome; Transcription;
Transcription regulation; Zinc; Zinc-finger.
CHAIN 1 910 Lysine-specific demethylase 7 homolog.
/FTId=PRO_0000399813.
DOMAIN 441 612 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
ZN_FING 208 290 PHD-type.
REGION 505 510 Substrate binding.
METAL 508 508 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538,
ECO:0000269|PubMed:20567261,
ECO:0000269|PubMed:21251613}.
METAL 510 510 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538,
ECO:0000269|PubMed:20567261,
ECO:0000269|PubMed:21251613}.
METAL 580 580 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538,
ECO:0000269|PubMed:20567261,
ECO:0000269|PubMed:21251613}.
BINDING 518 518 Substrate. {ECO:0000269|PubMed:21251613}.
BINDING 525 525 Substrate. {ECO:0000269|PubMed:21251613}.
BINDING 580 580 Substrate. {ECO:0000269|PubMed:21251613}.
VAR_SEQ 86 98 Missing (in isoform b). {ECO:0000305}.
/FTId=VSP_039912.
MUTAGEN 209 209 D->A: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 254 254 W->A: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 258 258 D->A: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 261 261 Q->A: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 263 263 W->A: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 402 402 D->A: Impairs histone methyltransferase
activity. {ECO:0000269|PubMed:20567261}.
MUTAGEN 409 409 Q->A: Impairs histone methyltransferase
activity. {ECO:0000269|PubMed:20567261}.
MUTAGEN 411 411 T->A: Impairs histone methyltransferase
activity. {ECO:0000269|PubMed:20567261}.
MUTAGEN 437 437 S->A: Abolishes histone methyltransferase
activity. {ECO:0000269|PubMed:20567261}.
MUTAGEN 495 495 F->A: Strongly impairs histone
methyltransferase activity.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 508 508 H->A: Fails to increase longevity.
{ECO:0000269|PubMed:27133168}.
MUTAGEN 510 510 D->A: Strongly impairs histone
methyltransferase activity.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 518 518 Y->A: Strongly impairs histone
methyltransferase activity.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 544 544 E->A: Impairs histone methyltransferase
activity. {ECO:0000269|PubMed:20567261}.
MUTAGEN 594 594 N->A: Strongly impairs histone
methyltransferase activity.
{ECO:0000269|PubMed:20567261}.
MUTAGEN 622 624 EKF->AAA: Abolishes histone
methyltransferase activity.
{ECO:0000269|PubMed:20567261}.
HELIX 207 209 {ECO:0000244|PDB:3N9N}.
TURN 212 214 {ECO:0000244|PDB:3PUR}.
TURN 244 249 {ECO:0000244|PDB:3PUR}.
STRAND 253 256 {ECO:0000244|PDB:3PUR}.
TURN 258 260 {ECO:0000244|PDB:3PUR}.
STRAND 263 265 {ECO:0000244|PDB:3PUR}.
HELIX 266 268 {ECO:0000244|PDB:3PUR}.
HELIX 273 275 {ECO:0000244|PDB:3PUR}.
TURN 276 278 {ECO:0000244|PDB:3PUR}.
STRAND 279 281 {ECO:0000244|PDB:3PUR}.
TURN 285 287 {ECO:0000244|PDB:3PUR}.
HELIX 288 291 {ECO:0000244|PDB:3PUR}.
STRAND 304 306 {ECO:0000244|PDB:3PUR}.
HELIX 310 312 {ECO:0000244|PDB:3PUR}.
HELIX 322 331 {ECO:0000244|PDB:3PUR}.
HELIX 332 334 {ECO:0000244|PDB:3PUR}.
TURN 340 342 {ECO:0000244|PDB:3PUR}.
STRAND 343 348 {ECO:0000244|PDB:3PUR}.
HELIX 349 358 {ECO:0000244|PDB:3PUR}.
HELIX 362 364 {ECO:0000244|PDB:3PUR}.
STRAND 367 373 {ECO:0000244|PDB:3PUR}.
HELIX 388 395 {ECO:0000244|PDB:3PUR}.
STRAND 400 405 {ECO:0000244|PDB:3PUR}.
TURN 406 409 {ECO:0000244|PDB:3PUR}.
STRAND 410 415 {ECO:0000244|PDB:3PUR}.
HELIX 416 424 {ECO:0000244|PDB:3PUR}.
STRAND 433 435 {ECO:0000244|PDB:3PUR}.
HELIX 446 449 {ECO:0000244|PDB:3PUR}.
HELIX 454 459 {ECO:0000244|PDB:3PUR}.
HELIX 461 465 {ECO:0000244|PDB:3PUR}.
HELIX 474 478 {ECO:0000244|PDB:3PUR}.
STRAND 479 481 {ECO:0000244|PDB:3PUR}.
HELIX 486 488 {ECO:0000244|PDB:3PUR}.
STRAND 493 499 {ECO:0000244|PDB:3PUR}.
STRAND 503 508 {ECO:0000244|PDB:3PUR}.
HELIX 511 513 {ECO:0000244|PDB:3PUR}.
STRAND 515 530 {ECO:0000244|PDB:3PUR}.
HELIX 534 545 {ECO:0000244|PDB:3PUR}.
HELIX 553 556 {ECO:0000244|PDB:3PUR}.
TURN 557 559 {ECO:0000244|PDB:3PUR}.
STRAND 562 567 {ECO:0000244|PDB:3PUR}.
STRAND 571 574 {ECO:0000244|PDB:3PUR}.
STRAND 579 595 {ECO:0000244|PDB:3PUR}.
HELIX 598 600 {ECO:0000244|PDB:3PUR}.
HELIX 601 617 {ECO:0000244|PDB:3PUR}.
HELIX 622 624 {ECO:0000244|PDB:3N9N}.
HELIX 629 639 {ECO:0000244|PDB:3PUR}.
HELIX 641 650 {ECO:0000244|PDB:3PUR}.
HELIX 656 683 {ECO:0000244|PDB:3PUR}.
HELIX 693 715 {ECO:0000244|PDB:3PUR}.
SEQUENCE 910 AA; 104672 MW; 8AE17DC5860EDFA5 CRC64;
MDGNDINIQK NEFSRDQSAL LMMDQHSDHK NHESAIGEPG MSYTASQPAL SSTEHQTPLV
SEASVAAPQN HLNGNSHESV SEMDRNSVDF AIESVLMKAR AYNKMGAPKD PRRKQHNPKS
EPKIEPHVTD SSDNQAAMSN KMEAEAPKME SNQNYVSNGS EPPFRFVSIS NFDEMKTKKK
EVQEELKLEV DSDSEEDDVP EQKTPKESDR CGGCGKFTHE DDLIALEEEK KKEKEKPLMS
KKKSHHHKKN DFQWIGCDSC QTWYHFLCSG LEQFEYYLYE KFFCPKCVPH TGHSIRYKVV
APHRYRWYSP NEKHLGIEVG SKTWIEDFIT RENTVPSPTD DEVCIVEDGY EFRREFEKLG
GADNWGKVFM VKDMDGLNMT MPKPGFDLED VVKIMGSDYE VDTIDVYNQS TYSMKLDTFR
KLFRDTKNRP LLYNFLSLEF SDNNEMKEIA KPPRFVQEIS MVNRLWPDVS GAEYIKLLQR
EEYLPEDQRP KVEQFCLAGM AGSYTDFHVD FGGSSVYYHI LKGEKIFYIA APTEQNFAAY
QAHETSPDTT TWFGDIANGA VKRVVIKEGQ TLLIPAGWIH AVLTPVDSLV FGGNFLHLGN
LEMQMRVYHL ENAIRKEIRS EEKFYFPNFE LLHWMYMRNV LLEKITEANQ EGSDMREQEK
NIWTASQIMK AEMERWMDRE LRLGPEKNAI LPTDDKNKIM ISVRKQIEIQ TKIQNAKNKP
MGLKQKRKSR ESAERDDEDY CPSSSTAYKK KYTKKAKKDN DDAPKVKKAK KEEVPEEKVP
VPEAAGPSEV TAPLTIKIGM GPTEDQKGVV QIFNNQCTSS GRKVKLNQNV ADYCGSHLEA
RVEEIPEKAT KSFRELDNEL ERCEAVHSGE KIKKVKEPKP PKQPKEKKEK PPPKKKEMSS
RDRLMKKLKM


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