PTM_ARATH
ID PTM_ARATH Reviewed; 1706 AA.
AC F4JYC8; F4JYC9; Q56XE1; Q9LHR7;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 81.
DE RecName: Full=DDT domain-containing protein PTM {ECO:0000305};
DE AltName: Full=DDT domain-containing protein 1 {ECO:0000305};
DE AltName: Full=Membrane-bound transcription factor PTM {ECO:0000305};
DE AltName: Full=PHD type transcription factor with transmembrane domains {ECO:0000303|PubMed:21934661};
GN Name=PTM {ECO:0000303|PubMed:21934661};
GN Synonyms=DDP1 {ECO:0000303|PubMed:23691993};
GN OrderedLocusNames=At5g35210 {ECO:0000312|Araport:AT5G35210};
GN ORFNames=K3D20.8 {ECO:0000312|EMBL:BAA98208.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1271-1539 (ISOFORM 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=21934661; DOI=10.1038/ncomms1486;
RA Sun X., Feng P., Xu X., Guo H., Ma J., Chi W., Lin R., Lu C., Zhang L.;
RT "A chloroplast envelope-bound PHD transcription factor mediates chloroplast
RT signals to the nucleus.";
RL Nat. Commun. 2:477-477(2011).
RN [5]
RP INTERACTION WITH CHR11.
RX PubMed=23691993; DOI=10.1111/jipb.12069;
RA Dong J., Gao Z., Liu S., Li G., Yang Z., Huang H., Xu L.;
RT "SLIDE, the protein interacting domain of Imitation Switch remodelers,
RT binds DDT-domain proteins of different subfamilies in chromatin remodeling
RT complexes.";
RL J. Integr. Plant Biol. 55:928-937(2013).
CC -!- FUNCTION: Membrane-bound transcription factor required for the plastid-
CC to-nucleus retrograde signaling. Functions in multiple retrograde
CC pathways. The plastid-to-nucleus signal plays an important role in the
CC coordinated expression of both nuclear- and chloroplast-localized genes
CC that encode photosynthesis-related proteins. In the nucleus, activates
CC ABI4 transcription in a PHD-dependent manner associated with histone
CC modifications. Localized primarily in the chloroplast outer membrane as
CC dormant form and, in response to retrograde signals, is released from
CC the membrane through proteolytic cleavage and its cleaved fragment
CC containing the transcription factor domain is redistributed to the
CC nucleus, where it regulates the expression of particular nuclear genes.
CC {ECO:0000269|PubMed:21934661}.
CC -!- SUBUNIT: Interacts (via the DDT domain) with CHR11 (via C-terminus).
CC {ECO:0000269|PubMed:23691993}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast outer membrane
CC {ECO:0000269|PubMed:21934661}; Multi-pass membrane protein
CC {ECO:0000255}. Nucleus {ECO:0000269|PubMed:21934661}. Note=Localized
CC primarily in the chloroplast outer membrane as dormant form and, upon
CC specific stimulation, is released from the membrane through proteolytic
CC cleavage, and its cleaved fragment containing the transcription factor
CC domain is redistributed to the nucleus, where it regulates the
CC expression of particular nuclear genes. {ECO:0000269|PubMed:21934661}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4JYC8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4JYC8-2; Sequence=VSP_058014, VSP_058015;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:21934661}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA98208.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD93752.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP002031; BAA98208.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93946.1; -; Genomic_DNA.
DR EMBL; AK221734; BAD93752.1; ALT_INIT; mRNA.
DR RefSeq; NP_198371.3; NM_122912.4. [F4JYC8-2]
DR AlphaFoldDB; F4JYC8; -.
DR SMR; F4JYC8; -.
DR STRING; 3702.AT5G35210.1; -.
DR MEROPS; M50.A02; -.
DR iPTMnet; F4JYC8; -.
DR PaxDb; F4JYC8; -.
DR PeptideAtlas; F4JYC8; -.
DR PRIDE; F4JYC8; -.
DR ProteomicsDB; 226434; -. [F4JYC8-1]
DR EnsemblPlants; AT5G35210.1; AT5G35210.1; AT5G35210.
DR EnsemblPlants; AT5G35210.2; AT5G35210.2; AT5G35210. [F4JYC8-2]
DR GeneID; 833475; -.
DR Gramene; AT5G35210.1; AT5G35210.1; AT5G35210.
DR Gramene; AT5G35210.2; AT5G35210.2; AT5G35210. [F4JYC8-2]
DR KEGG; ath:AT5G35210; -.
DR Araport; AT5G35210; -.
DR TAIR; locus:2182437; AT5G35210.
DR eggNOG; KOG1473; Eukaryota.
DR InParanoid; F4JYC8; -.
DR OMA; MEYEMDS; -.
DR PRO; PR:F4JYC8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4JYC8; baseline and differential.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009707; C:chloroplast outer membrane; IDA:UniProtKB.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0031010; C:ISWI-type complex; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:TAIR.
DR GO; GO:0010019; P:chloroplast-nucleus signaling pathway; IDA:TAIR.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:TAIR.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR018501; DDT_dom.
DR InterPro; IPR028942; WHIM1_dom.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF02791; DDT; 1.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF15612; WHIM1; 1.
DR SMART; SM00571; DDT; 1.
DR SMART; SM00249; PHD; 4.
DR SUPFAM; SSF57903; SSF57903; 3.
DR PROSITE; PS50827; DDT; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Membrane; Metal-binding; Nucleus;
KW Plastid; Plastid outer membrane; Reference proteome; Repeat; Transcription;
KW Transcription regulation; Transmembrane; Transmembrane helix; Zinc;
KW Zinc-finger.
FT CHAIN 1..1706
FT /note="DDT domain-containing protein PTM"
FT /id="PRO_0000435121"
FT TRANSMEM 1539..1559
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 1569..1589
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 1596..1616
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 1624..1644
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 1682..1702
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 192..252
FT /note="DDT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00063"
FT ZN_FING 411..458
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 144..168
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 375..408
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1165..1194
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1311..1345
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 9..18
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 375..389
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 390..407
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1166..1194
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1311..1325
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1537..1539
FT /note="IRA -> EWQ (in isoform 2)"
FT /id="VSP_058014"
FT VAR_SEQ 1540..1706
FT /note="Missing (in isoform 2)"
FT /id="VSP_058015"
FT CONFLICT 1334
FT /note="D -> G (in Ref. 3; BAD93752)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1706 AA; 189210 MW; 8EA504D21BD5263F CRC64;
MEAKVPRPRG RPRKRQRLED DNRKLNNRGK KQVLEVEPAV PISLLGCYML KDFDDNEVFL
GKIVSYDTGL YRVIYEDGDC EELESGDLRR LIISDSYLDD ELRVRRKKLD KLILKKEEKK
KRNSPENKAV ELPNQVNGVQ ARAVTNSEDG DSYSDSESSE SGDKRGSDLE IEAPLVPPVD
LPPSSGTIGI PEEAVAHLLS VYGFLRSFSF QLYICPFELN DFVGALYFSG PNSLLDAVHV
ALLRALKGHL ERLSSSKSVL ASKCLRCIDW SLLDVLTWPV YLVQYFTAMG HASGPQWNIF
NKFVVEIEYY SLPIGMKLKI LQILCDDIFD VADLRDEIDA REESEIGFDP DRVATGLLEN
VPRRVHPRFA KTSAYKEKEV TDSSTNESKD LDSRCTNGGS NEVSSDLDGN SDECRICGMD
GTLLCCDGCP LAYHSRCIGV VKMYIPDGPW FCPECTINKK GPKIAHGTSL RGAVQFGMDP
HGRLFLGTCN HLLVLNISVN GDAVVKYYNV NDISKVVLVL ISASSHTLEY VEICKAITQY
WDLPEGISLR EGEIGLTQAK DREDGKVSEI TKSDSANISN RSHTQTVFDL PTSTLGNTNS
AVTGGSCGIQ GKKLAARVTY LGLSFKPNTY NNHYTNGELA VSAAASLAVL SSEETHEPDL
RKYNSAKKAA SSNILEQMKA FSLVAPRFFW PSPDKKEITR ERCGWCHSCR LTSASRRGCM
LNAAVAGATK GAMKIFSGLF PLKNGEGVLS SIAAYILYLE ESLRGLIAGP FLSESPRKQW
RKQVEEASTC KALKAPLLEL EENICSIALS CDWFKQMDDW LIEHSIFQSA PVTLGVPQRR
GPGRTKQNTQ AEVTAEGSDA DSFTWWRGGK LSKVILLKAV LSQPATKKAA WQGGSKKIPG
LNYGDASYIP RRSRRSFWKA AVESSKNISQ LALQVRYLDM SLRWRELVRP DQNLQNVKGP
ETDVAIFRNA RICDKKLSDN KVSYGVFFGN QKHLPSRVMK NIMEVEKTQD RNEKYWLQEA
HVPLYLIKEF EESLHRVQMP SSTKKPSKKL SKLQRKQLKA SLMDIFSYIA SRRDKMEKCS
CASCDHDVLL RDTTTCSSCH GFCHKDCTSM SQHTNGNVEV LVTCKRCYLS KTRVPTNINH
RQSTAPQFTI NVRHQNAVIP VIKVKPPSQQ LSSQKPRENT SGVKQVTPDS SVSKSKQKTL
SCGVIWRKKN VEDTGVDFRN QNILLAGRSD KPSLEPVCGI CLLPYNPGLT YIHCTKCEKW
FHTEAVKLKD SQIPEVVGFK CCKCRRIRSP DCPYMDPKLK EQKQIKRIVF TNQKQRQGNS
GLDSDSERMS EQKDSKPSTP LPATPLYPPD DVFIPEDDPL LVSVSKVKQI TPSSFDLEWS
TTAFAPGPQK LPVRRQVKRE DSDAAYPELH PIVKPEAEEQ ALPVLTEWDL SGELLFDYED
MEFEPQTYFS LTELLTADDS GGGQYQENGD MVVSGNPQFE PTEKEECEDD MGPCQRCLQM
DPAPDLLCTV CGLLIHSHCS PWSALPGSSW SCGQCRIRAL GSITLGSFGA ITQFKSILPD
RSTKVDISLA GPFAGAALSV SMFAVGLFLS TEPDAANDLV QVPSMLFQGS LLLGLISRAT
LGYAALHAAT VSIHPLVIAG WCGLTTTAFN MLPVGCLDGG RAVQGAFGKN ALVTFGLSTY
VMLGLRVLGG PLALPWGLYV LICRNT
