APD3_ARATH
ID APD3_ARATH Reviewed; 404 AA.
AC B3H754; A0A1P8AYU1; O80447;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=E3 ubiquitin-protein ligase APD3 {ECO:0000305};
DE EC=2.3.2.27 {ECO:0000250|UniProtKB:Q6DBH0};
DE AltName: Full=Protein ABERRANT POLLEN DEVELOPMENT 3 {ECO:0000303|PubMed:22897245};
GN Name=APD3 {ECO:0000303|PubMed:22897245};
GN OrderedLocusNames=At2g38220 {ECO:0000312|Araport:AT2G38220};
GN ORFNames=F16M14.15 {ECO:0000312|EMBL:AAC27171.1};
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 FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP 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:0000250|UniProtKB:Q0WS06}; Multi-pass membrane protein
CC {ECO:0000255}. Vacuole membrane {ECO:0000250|UniProtKB:Q0WS06}; Multi-
CC pass membrane protein {ECO:0000255}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=B3H754-1; Sequence=Displayed;
CC Name=2;
CC IsoId=B3H754-2; Sequence=VSP_060126;
CC -!- TISSUE SPECIFICITY: Expressed in the shoot apical meristems (SAM), root
CC tips, pollen and inflorescences. {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 observed only in young floral buds and seeds (PubMed:22897245).
CC Accumulates at the late bicellular pollen stage and levels gradually
CC strengthened from the tricellular pollen stage to the mature pollen
CC stage (PubMed:22897245). {ECO:0000269|PubMed:22897245}.
CC -!- DISRUPTION PHENOTYPE: Plants lacking APD1, APD2, APD3 and APD4 are
CC defective for cell division in male gametogenesis resulting in severe
CC abnormal bicellular-like pollen phenotypes.
CC {ECO:0000269|PubMed:22897245}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC27171.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC003028; AAC27171.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC09510.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM61826.1; -; Genomic_DNA.
DR PIR; T01254; T01254.
DR RefSeq; NP_001324023.1; NM_001336694.1. [B3H754-2]
DR RefSeq; NP_181357.2; NM_129379.2. [B3H754-1]
DR AlphaFoldDB; B3H754; -.
DR SMR; B3H754; -.
DR STRING; 3702.AT2G38220.1; -.
DR PaxDb; B3H754; -.
DR EnsemblPlants; AT2G38220.1; AT2G38220.1; AT2G38220. [B3H754-1]
DR EnsemblPlants; AT2G38220.2; AT2G38220.2; AT2G38220. [B3H754-2]
DR GeneID; 818401; -.
DR Gramene; AT2G38220.1; AT2G38220.1; AT2G38220. [B3H754-1]
DR Gramene; AT2G38220.2; AT2G38220.2; AT2G38220. [B3H754-2]
DR KEGG; ath:AT2G38220; -.
DR Araport; AT2G38220; -.
DR TAIR; locus:2042922; AT2G38220.
DR eggNOG; KOG4275; Eukaryota.
DR HOGENOM; CLU_040868_1_0_1; -.
DR InParanoid; B3H754; -.
DR OrthoDB; 1361306at2759; -.
DR PhylomeDB; B3H754; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:B3H754; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; B3H754; baseline and differential.
DR GO; GO:0005768; C:endosome; ISS:UniProtKB.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0009705; C:plant-type vacuole membrane; ISS: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:TAIR.
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; 2.
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..404
FT /note="E3 ubiquitin-protein ligase APD3"
FT /id="PRO_0000446986"
FT TRANSMEM 42..62
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 289..309
FT /note="Helical"
FT /evidence="ECO:0000255"
FT ZN_FING 353..392
FT /note="RING-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT VAR_SEQ 162..164
FT /note="Missing (in isoform 2)"
FT /id="VSP_060126"
SQ SEQUENCE 404 AA; 45067 MW; E9F2E8B352802B14 CRC64;
MGSIRGDLQP LFVMPPPPLD EDCDDIFNSD ESSWGLLSLS CFGIIMGLWF FASVCLIFGV
YGSETVWLGP NSSILVKPSS IFVKSIKVKE LDFSKPGLQL YGFNGQSTPS GYFVNWTESR
VLSVSQNSYK GWPYYLNRGT HMNISYNILP KGSAVRLVIT EGSQVIGMPF FYRSSLKDIA
FRDTAWSWNL IQGSGMIQLD ISKSKGYYLT VANLKRKDIE VELDIDVKAV LYDTKQTSYN
CSFSNGECSF KMNERYPVEN YAVVTSPALG QGVSIDDEWY IELSYQPRLI AYGSFTGVLL
SFMLVAIHFC NKLKCCGGEG FLSGDDSVRT CLLADKGDND CCNDVEASNK SLCAICFDAP
RDCCFLPCGH CVSCYQCGTK IKRTKGRCPI CRKKMIHVKR IYTA
