ID   APD1_ARATH              Reviewed;         441 AA.
AC   Q0WS06; F4IS11; Q8S8T1;
DT   08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT   05-SEP-2006, sequence version 1.
DT   25-MAY-2022, entry version 117.
DE   RecName: Full=E3 ubiquitin-protein ligase APD1 {ECO:0000305};
DE            EC=2.3.2.27 {ECO:0000250|UniProtKB:Q6DBH0};
DE   AltName: Full=Protein ABERRANT POLLEN DEVELOPMENT 1 {ECO:0000303|PubMed:22897245};
GN   Name=APD1 {ECO:0000303|PubMed:22897245};
GN   OrderedLocusNames=At2g38185 {ECO:0000312|Araport:AT2G38185};
GN   ORFNames=F16M14 {ECO:0000312|EMBL:AAM14856.1};
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;
RX   PubMed=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA   Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA   Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA   Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA   Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL   Nature 402:761-768(1999).
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] (ISOFORM 1).
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RA   Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA   Feldmann K.A.;
RT   "Full-length cDNA from Arabidopsis thaliana.";
RL   Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP   DEVELOPMENTAL STAGE, GENE FAMILY, AND NOMENCLATURE.
RC   STRAIN=cv. Columbia;
RX   PubMed=22897245; DOI=10.1111/j.1744-7909.2012.01152.x;
RA   Luo G., Gu H., Liu J., Qu L.-J.;
RT   "Four closely-related RING-type E3 ligases, APD1-4, are involved in pollen
RT   mitosis II regulation in Arabidopsis.";
RL   J. Integr. Plant Biol. 54:814-827(2012).
CC   -!- FUNCTION: Involved in pollen mitosis II (PMII) regulation during male
CC       gametogenesis. {ECO:0000269|PubMed:22897245}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC         [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC         cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC         EC=2.3.2.27; Evidence={ECO:0000250|UniProtKB:Q6DBH0};
CC   -!- PATHWAY: Protein modification; protein ubiquitination.
CC       {ECO:0000250|UniProtKB:Q6DBH0}.
CC   -!- SUBCELLULAR LOCATION: Endomembrane system
CC       {ECO:0000269|PubMed:22897245}; Multi-pass membrane protein
CC       {ECO:0000255}. Vacuole membrane {ECO:0000269|PubMed:22897245}; Multi-
CC       pass membrane protein {ECO:0000255}. Note=Associated with intracellular
CC       membranes and in the tonoplast and endosomes in the germinating pollen
CC       tubes. {ECO:0000269|PubMed:22897245}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1;
CC         IsoId=Q0WS06-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q0WS06-2; Sequence=VSP_060124, VSP_060125;
CC       Name=3;
CC         IsoId=Q0WS06-3; Sequence=VSP_060123;
CC   -!- TISSUE SPECIFICITY: Expressed in the shoot apical meristems (SAM), root
CC       tips and inflorescences, and, at low levels, in floral buds and pollen.
CC       {ECO:0000269|PubMed:22897245}.
CC   -!- DEVELOPMENTAL STAGE: In young seedlings, expressed in the shoot apical
CC       meristem (SAM) and in root tips (PubMed:22897245). In inflorescence,
CC       highly observed in the pistil and in seeds, but weakly present during
CC       male gametogenesis (PubMed:22897245). Observed at very weak levels from
CC       the late bicellular pollen stage to the mature pollen stage
CC       (PubMed:22897245). Detected in the germinating pollen tubes
CC       (PubMed:22897245). {ECO:0000269|PubMed:22897245}.
CC   -!- DISRUPTION PHENOTYPE: No obvious defects during the vegetative
CC       developmental stage (PubMed:22897245). The double mutant lacking both
CC       APD1 and APD2 exhibits an increased percentage of bicellular-like
CC       pollen at the mature pollen stage (PubMed:22897245). Plants lacking
CC       APD1, APD2, APD3 and APD4 are defective for cell division in male
CC       gametogenesis resulting in severe abnormal bicellular-like pollen
CC       phenotypes (PubMed:22897245). {ECO:0000269|PubMed:22897245}.
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DR   EMBL; AC003028; AAM14856.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC09503.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC09504.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC09505.1; -; Genomic_DNA.
DR   EMBL; AK228136; BAF00093.1; -; mRNA.
DR   EMBL; AY086581; AAM63643.1; -; mRNA.
DR   RefSeq; NP_565884.2; NM_129375.3. [Q0WS06-1]
DR   RefSeq; NP_973631.1; NM_201902.4. [Q0WS06-1]
DR   RefSeq; NP_973632.1; NM_201903.2. [Q0WS06-3]
DR   AlphaFoldDB; Q0WS06; -.
DR   SMR; Q0WS06; -.
DR   STRING; 3702.AT2G38185.4; -.
DR   ProteomicsDB; 191193; -. [Q0WS06-1]
DR   ProteomicsDB; 206360; -.
DR   EnsemblPlants; AT2G38185.1; AT2G38185.1; AT2G38185. [Q0WS06-1]
DR   EnsemblPlants; AT2G38185.2; AT2G38185.2; AT2G38185. [Q0WS06-1]
DR   EnsemblPlants; AT2G38185.3; AT2G38185.3; AT2G38185. [Q0WS06-3]
DR   GeneID; 818397; -.
DR   Gramene; AT2G38185.1; AT2G38185.1; AT2G38185. [Q0WS06-1]
DR   Gramene; AT2G38185.2; AT2G38185.2; AT2G38185. [Q0WS06-1]
DR   Gramene; AT2G38185.3; AT2G38185.3; AT2G38185. [Q0WS06-3]
DR   KEGG; ath:AT2G38185; -.
DR   Araport; AT2G38185; -.
DR   PhylomeDB; Q0WS06; -.
DR   UniPathway; UPA00143; -.
DR   PRO; PR:Q0WS06; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q0WS06; baseline and differential.
DR   GO; GO:0005768; C:endosome; IDA:UniProtKB.
DR   GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR   GO; GO:0009705; C:plant-type vacuole membrane; IDA:UniProtKB.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0004842; F:ubiquitin-protein transferase activity; IEA:InterPro.
DR   GO; GO:0000278; P:mitotic cell cycle; IMP:UniProtKB.
DR   GO; GO:0009555; P:pollen development; IMP:UniProtKB.
DR   Gene3D; 3.30.40.10; -; 1.
DR   InterPro; IPR044586; APD1/2/3/4.
DR   InterPro; IPR032008; DUF4792.
DR   InterPro; IPR032010; DUF4793.
DR   InterPro; IPR001841; Znf_RING.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   PANTHER; PTHR46858; PTHR46858; 1.
DR   Pfam; PF16040; DUF4792; 1.
DR   Pfam; PF16041; DUF4793; 1.
DR   SMART; SM00184; RING; 1.
DR   PROSITE; PS50089; ZF_RING_2; 1.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Membrane; Metal-binding; Reference proteome;
KW   Transferase; Transmembrane; Transmembrane helix; Ubl conjugation pathway;
KW   Vacuole; Zinc; Zinc-finger.
FT   CHAIN           1..441
FT                   /note="E3 ubiquitin-protein ligase APD1"
FT                   /id="PRO_0000446984"
FT   TRANSMEM        60..80
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        305..325
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   ZN_FING         390..429
FT                   /note="RING-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT   VAR_SEQ         1..159
FT                   /note="MDSAPSPSSLDFELSPPVLVTMTSTSSSASDNVEGADDDANTHGIFNWRDFS
FT                   SCWRVSESNLYCFSLALLIWFFASFILIENLYGPKNVWLGPSSSILVEPSSIFVKSIKV
FT                   KVLDYSEPGLQLYGFYRTPALDCFVNWSESRVLSISHESYKGWPYYLN -> MSGLDPV
FT                   RQFLLNQALFLSKALRLKCLITQNQGFSFMGSIELLLWIVLSTGLNPECYLSHMNLT
FT                   (in isoform 3)"
FT                   /id="VSP_060123"
FT   VAR_SEQ         153..193
FT                   /note="GWPYYLNSGSLLNITYTVKPQGSAVQLVVDEGHQGVPQSVL -> VALRFSV
FT                   LFSLKCIYGWFLNFMRTFIVLIRSVVFVYFTLIF (in isoform 2)"
FT                   /id="VSP_060124"
FT   VAR_SEQ         194..441
FT                   /note="Missing (in isoform 2)"
FT                   /id="VSP_060125"
SQ   SEQUENCE   441 AA;  49058 MW;  6EF38BE15C74B3A0 CRC64;
     MDSAPSPSSL DFELSPPVLV TMTSTSSSAS DNVEGADDDA NTHGIFNWRD FSSCWRVSES
     NLYCFSLALL IWFFASFILI ENLYGPKNVW LGPSSSILVE PSSIFVKSIK VKVLDYSEPG
     LQLYGFYRTP ALDCFVNWSE SRVLSISHES YKGWPYYLNS GSLLNITYTV KPQGSAVQLV
     VDEGHQGVPQ SVLNDPAYRY NVWSWNLIEG SGMIQLEIRK SSSYYLAVAN LKSKDVEVEL
     NIDVKAVLYD TKQSFYNCNF SNGECTFNAM SLVGNSVVVT SPAASQGVSI EDEWYIRFSY
     QPREIAYVIG TGVVICFMLV AIQFCNRFQC SGGEGHLTED DSARTRLLAD KDDDGSSMGS
     CDDSYANDDA DLEEFMGNDG EASNRSRRLC AICFDVPRDC FFLPCGHSVS CYECGTTMQE
     ADGSCPICRR KMKKVKRIYT V