APD4_ARATH
ID APD4_ARATH Reviewed; 399 AA.
AC F4ISV9; F4IS12; O80445; Q4PL85; Q84RL2;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=E3 ubiquitin-protein ligase APD4 {ECO:0000305};
DE EC=2.3.2.27 {ECO:0000250|UniProtKB:Q6DBH0};
DE AltName: Full=Protein ABERRANT POLLEN DEVELOPMENT 4 {ECO:0000303|PubMed:22897245};
GN Name=APD4 {ECO:0000303|PubMed:22897245};
GN OrderedLocusNames=At2g38195 {ECO:0000312|Araport:AT2G38195};
GN ORFNames=F16M14.13 {ECO:0000312|EMBL:AAO86831.1};
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] (ISOFORMS 2 AND 3).
RC STRAIN=cv. Columbia;
RX PubMed=16244158; DOI=10.1104/pp.105.063479;
RA Xiao Y.-L., Smith S.R., Ishmael N., Redman J.C., Kumar N., Monaghan E.L.,
RA Ayele M., Haas B.J., Wu H.C., Town C.D.;
RT "Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2
RT reveals numerous transcript variants.";
RL Plant Physiol. 139:1323-1337(2005).
RN [4]
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=3;
CC Name=1;
CC IsoId=F4ISV9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4ISV9-2; Sequence=VSP_060128;
CC Name=3;
CC IsoId=F4ISV9-3; Sequence=VSP_060127;
CC -!- TISSUE SPECIFICITY: Expressed in the shoot apical meristems (SAM), root
CC tips 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 detected in young floral buds, carpels and seeds (PubMed:22897245).
CC {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=AAC27169.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC003028; AAC27169.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC09507.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09508.1; -; Genomic_DNA.
DR EMBL; AY231403; AAO86831.1; -; mRNA.
DR EMBL; DQ069803; AAY82262.1; -; mRNA.
DR PIR; T01252; T01252.
DR RefSeq; NP_001118467.1; NM_001124995.1. [F4ISV9-2]
DR RefSeq; NP_001118468.1; NM_001124996.1. [F4ISV9-1]
DR AlphaFoldDB; F4ISV9; -.
DR SMR; F4ISV9; -.
DR STRING; 3702.AT2G38195.1; -.
DR PaxDb; F4ISV9; -.
DR PRIDE; F4ISV9; -.
DR EnsemblPlants; AT2G38195.1; AT2G38195.1; AT2G38195. [F4ISV9-1]
DR EnsemblPlants; AT2G38195.2; AT2G38195.2; AT2G38195. [F4ISV9-2]
DR GeneID; 6240532; -.
DR Gramene; AT2G38195.1; AT2G38195.1; AT2G38195. [F4ISV9-1]
DR Gramene; AT2G38195.2; AT2G38195.2; AT2G38195. [F4ISV9-2]
DR KEGG; ath:AT2G38195; -.
DR Araport; AT2G38195; -.
DR TAIR; locus:4515102961; AT2G38195.
DR eggNOG; KOG4275; Eukaryota.
DR HOGENOM; CLU_040868_1_0_1; -.
DR InParanoid; F4ISV9; -.
DR OrthoDB; 1361306at2759; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:F4ISV9; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; F4ISV9; 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..399
FT /note="E3 ubiquitin-protein ligase APD4"
FT /id="PRO_0000446987"
FT TRANSMEM 42..62
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 284..304
FT /note="Helical"
FT /evidence="ECO:0000255"
FT ZN_FING 348..387
FT /note="RING-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT VAR_SEQ 1..215
FT /note="MGSIRGDLQPLFVMPPPPLDEDCDDIFNSDESSWGLLSLSCFGIIMGLWFFA
FT SVCLIFGVYGSETVWLGPNSSILVKPSSIFVKSINAKELDFSKPGLQLYGFNGQSTPSG
FT YFVNWTESRVLSVSQNSYKGWPYYLNRGTHMNISYNILPKGSAVRLVITEGMPFFYRSS
FT LKDIAFRDTAWSWNLIQGSGMIQLDISKSKGYYLTVANLKRKDVE -> MFVQ (in
FT isoform 3)"
FT /id="VSP_060127"
FT VAR_SEQ 2..87
FT /note="GSIRGDLQPLFVMPPPPLDEDCDDIFNSDESSWGLLSLSCFGIIMGLWFFAS
FT VCLIFGVYGSETVWLGPNSSILVKPSSIFVKSIN -> SKENEESEANLYS (in
FT isoform 2)"
FT /id="VSP_060128"
FT CONFLICT 224
FT /note="V -> A (in Ref. 3; AAO86831)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 399 AA; 44536 MW; 70506AD0473FE1B7 CRC64;
MGSIRGDLQP LFVMPPPPLD EDCDDIFNSD ESSWGLLSLS CFGIIMGLWF FASVCLIFGV
YGSETVWLGP NSSILVKPSS IFVKSINAKE LDFSKPGLQL YGFNGQSTPS GYFVNWTESR
VLSVSQNSYK GWPYYLNRGT HMNISYNILP KGSAVRLVIT EGMPFFYRSS LKDIAFRDTA
WSWNLIQGSG MIQLDISKSK GYYLTVANLK RKDVEVELDI DVKVVLYDTK QSSYNCSFSN
GECSFKMNER SPVENYAVVT SPALGQGVSI DDEWYIELSY QPRLIAYGSF TGVLLSFMLV
AIHFCNKLKC CGGEGFLSED DSVRTCLLAD KGDNDCCNDV EASNKSLCAI CFDAPRDCCF
LPCGHCVSCY QCGTKIKRTK GRCPICRKKI MHVKRIYTA
