APD2_ARATH
ID APD2_ARATH Reviewed; 444 AA.
AC Q6DBH0; Q9M029;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=E3 ubiquitin-protein ligase APD2 {ECO:0000305};
DE EC=2.3.2.27 {ECO:0000269|PubMed:22897245};
DE AltName: Full=Protein ABERRANT POLLEN DEVELOPMENT 2 {ECO:0000303|PubMed:22897245};
GN Name=APD2 {ECO:0000303|PubMed:22897245};
GN OrderedLocusNames=At5g01450 {ECO:0000312|Araport:AT5G01450};
GN ORFNames=T10O8.160 {ECO:0000312|EMBL:CAB81928.1};
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=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
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].
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Cheuk R.F., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [5]
RP FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, PATHWAY, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INTERACTION WITH
RP AT1G78040; AT1G10650; VHA-C4/AVAP4; VHA-C''2/VMA16 AND TUFA, GENE FAMILY,
RP 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: Exhibits E2-dependent E3 ligase activity (PubMed:22897245).
CC Involved in pollen mitosis II (PMII) regulation during male
CC gametogenesis (PubMed:22897245). {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:0000269|PubMed:22897245};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000269|PubMed:22897245}.
CC -!- SUBUNIT: Interacts with At1g78040, At1g10650, VHA-c4/AVAP4, VHA-
CC c''2/VMA16 and TUFA. {ECO:0000269|PubMed:22897245}.
CC -!- SUBCELLULAR LOCATION: Endomembrane system
CC {ECO:0000269|PubMed:22897245}; Multi-pass membrane protein
CC {ECO:0000255}. Note=Associated with intracellular membranes and in the
CC tonoplast and endosomes in the germinating pollen tubes.
CC {ECO:0000269|PubMed:22897245}.
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 specifically observed in mature pollen (PubMed:22897245). Present from
CC the early bicellular pollen stage to the mature pollen stage; levels in
CC vegetative cells increase during the development of pollen
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB81928.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL161746; CAB81928.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED90346.1; -; Genomic_DNA.
DR EMBL; BT015052; AAT71924.1; -; mRNA.
DR EMBL; BT015858; AAU94421.1; -; mRNA.
DR EMBL; AK229004; BAF00891.1; -; mRNA.
DR PIR; T48167; T48167.
DR RefSeq; NP_195765.3; NM_120223.5.
DR AlphaFoldDB; Q6DBH0; -.
DR SMR; Q6DBH0; -.
DR STRING; 3702.AT5G01450.1; -.
DR iPTMnet; Q6DBH0; -.
DR PaxDb; Q6DBH0; -.
DR PRIDE; Q6DBH0; -.
DR ProteomicsDB; 185190; -.
DR EnsemblPlants; AT5G01450.1; AT5G01450.1; AT5G01450.
DR GeneID; 831860; -.
DR Gramene; AT5G01450.1; AT5G01450.1; AT5G01450.
DR KEGG; ath:AT5G01450; -.
DR Araport; AT5G01450; -.
DR TAIR; locus:2179187; AT5G01450.
DR eggNOG; KOG4275; Eukaryota.
DR HOGENOM; CLU_040868_1_0_1; -.
DR InParanoid; Q6DBH0; -.
DR OMA; HNTTNAY; -.
DR OrthoDB; 606561at2759; -.
DR PhylomeDB; Q6DBH0; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q6DBH0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q6DBH0; 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; IDA:UniProtKB.
DR GO; GO:0000278; P:mitotic cell cycle; IMP:TAIR.
DR GO; GO:0009555; P:pollen development; IMP:UniProtKB.
DR GO; GO:0016567; P:protein ubiquitination; IDA: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 PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW Membrane; Metal-binding; Reference proteome; Transferase; Transmembrane;
KW Transmembrane helix; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..444
FT /note="E3 ubiquitin-protein ligase APD2"
FT /id="PRO_0000446985"
FT TRANSMEM 74..94
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 312..332
FT /note="Helical"
FT /evidence="ECO:0000255"
FT ZN_FING 393..432
FT /note="RING-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 1..41
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 20..41
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 444 AA; 49277 MW; F5AEB1A9DEE27241 CRC64;
MSLPDSLPSS SSSPPVTREE TGFHRFEHHG NDSGFDHRDR PPWNRSEYDY RHGSVVASEN
VRNNSTSEDP WSCVVVVATF CIFVSMTLIL GLYGTTNVWL GPNSSFLIKP TSVFVQNVIV
EELGNKGSGL ILYGLNQAPQ LDVLTKWSEV HYLAVPNDSY KYWIQYLNKG SRVKVSYNVE
SVGSSLYLVI AQGVDGLSEW VQDPTRPDTT LSWHIISDSG YIEQDITKSS SYYVAVGNVY
LNEVKATIDI QVEGVLYDTT NAYYNCSFPN DKCTLSVPLF GTNAAVLTSP GPKLNNSKNE
FCAKLSYEPR WIAYIVCMGV VTALLLIVSS LFNKRQPVTE DETVDENDDV APLIPGKDDD
NSSWCSSYSS ILTSTEELEG AHGEGHSSTR YLCAICYDAP RDCFFLSCGH CVACFQCGTR
IAETSGFCPV CRKKIRKVKK IFNV
