AGD5_ARATH
ID AGD5_ARATH Reviewed; 483 AA.
AC Q9FL69; C4NZX2; Q8L8M0; Q9FVH4;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 127.
DE RecName: Full=ADP-ribosylation factor GTPase-activating protein AGD5 {ECO:0000303|PubMed:12644670};
DE Short=ARF GAP AGD5 {ECO:0000303|PubMed:12644670};
DE AltName: Full=Protein ARF-GAP DOMAIN 5 {ECO:0000303|PubMed:12644670};
DE Short=AtAGD5 {ECO:0000303|PubMed:12644670};
DE AltName: Full=Protein MODIFIED TRANSPORT TO THE VACUOLE 4 {ECO:0000303|PubMed:23771894};
DE AltName: Full=Protein NEVERSHED {ECO:0000303|PubMed:19429787};
DE AltName: Full=Protein ZIGA3 {ECO:0000303|PubMed:11202441};
GN Name=AGD5 {ECO:0000303|PubMed:12644670};
GN Synonyms=MTV4 {ECO:0000303|PubMed:23771894},
GN NEV {ECO:0000303|PubMed:19429787}, ZIG3 {ECO:0000303|PubMed:11202441},
GN ZIGA3 {ECO:0000303|PubMed:11202441};
GN OrderedLocusNames=At5g54310 {ECO:0000312|Araport:AT5G54310};
GN ORFNames=MDK4.13 {ECO:0000312|EMBL:BAB10754.1};
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 [MRNA], FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF
RP CYS-34; CYS-51 AND ARG-59, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=19429787; DOI=10.1242/dev.033605;
RA Liljegren S.J., Leslie M.E., Darnielle L., Lewis M.W., Taylor S.M., Luo R.,
RA Geldner N., Chory J., Randazzo P.A., Yanofsky M.F., Ecker J.R.;
RT "Regulation of membrane trafficking and organ separation by the NEVERSHED
RT ARF-GAP protein.";
RL Development 136:1909-1918(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9679202; DOI=10.1093/dnares/5.2.131;
RA Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
RT features of the regions of 1,381,565 bp covered by twenty one physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:131-145(1998).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [6]
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 [7]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 7-483.
RC STRAIN=cv. Columbia;
RX PubMed=11202441; DOI=10.1023/a:1026509002161;
RA Jensen R.B., Lykke-Andersen K., Frandsen G.I., Nielsen H.B., Haseloff J.,
RA Jespersen H.M., Mundy J., Skriver K.;
RT "Promiscuous and specific phospholipid binding by domains in ZAC, a
RT membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a
RT C2 domain.";
RL Plant Mol. Biol. 44:799-814(2000).
RN [8]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=12644670; DOI=10.1104/pp.013052;
RA Vernoud V., Horton A.C., Yang Z., Nielsen E.;
RT "Analysis of the small GTPase gene superfamily of Arabidopsis.";
RL Plant Physiol. 131:1191-1208(2003).
RN [9]
RP NOT SURE.
RX PubMed=16731582; DOI=10.1104/pp.106.077818;
RA Song X.-F., Yang C.-Y., Liu J., Yang W.-C.;
RT "RPA, a class II ARFGAP protein, activates ARF1 and U5 and plays a role in
RT root hair development in Arabidopsis.";
RL Plant Physiol. 141:966-976(2006).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=20081191; DOI=10.1242/dev.041335;
RA Leslie M.E., Lewis M.W., Youn J.-Y., Daniels M.J., Liljegren S.J.;
RT "The EVERSHED receptor-like kinase modulates floral organ shedding in
RT Arabidopsis.";
RL Development 137:467-476(2010).
RN [12]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=20230490; DOI=10.1111/j.1365-313x.2010.04194.x;
RA Lewis M.W., Leslie M.E., Fulcher E.H., Darnielle L., Healy P.N.,
RA Youn J.-Y., Liljegren S.J.;
RT "The SERK1 receptor-like kinase regulates organ separation in Arabidopsis
RT flowers.";
RL Plant J. 62:817-828(2010).
RN [13]
RP FUNCTION, MUTAGENESIS OF ARG-59, SUBCELLULAR LOCATION, AND INTERACTION WITH
RP ARF1.
RC STRAIN=cv. Columbia;
RX PubMed=21105926; DOI=10.1111/j.1365-313x.2010.04369.x;
RA Stefano G., Renna L., Rossi M., Azzarello E., Pollastri S., Brandizzi F.,
RA Baluska F., Mancuso S.;
RT "AGD5 is a GTPase-activating protein at the trans-Golgi network.";
RL Plant J. 64:790-799(2010).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. C24, cv. Columbia, and cv. Landsberg erecta;
RX PubMed=23963677; DOI=10.1093/jxb/ert232;
RA Liu B., Butenko M.A., Shi C.-L., Bolivar J.L., Winge P., Stenvik G.-E.,
RA Vie A.K., Leslie M.E., Brembu T., Kristiansen W., Bones A.M.,
RA Patterson S.E., Liljegren S.J., Aalen R.B.;
RT "NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially
RT required for cell expansion and cell separation during floral organ
RT abscission in Arabidopsis thaliana.";
RL J. Exp. Bot. 64:5345-5357(2013).
RN [15]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, INTERACTION WITH
RP CLATHRIN, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia;
RX PubMed=23771894; DOI=10.1105/tpc.113.111724;
RA Sauer M., Delgadillo M.O., Zouhar J., Reynolds G.D., Pennington J.G.,
RA Jiang L., Liljegren S.J., Stierhof Y.-D., De Jaeger G., Otegui M.S.,
RA Bednarek S.Y., Rojo E.;
RT "MTV1 and MTV4 encode plant-specific ENTH and ARF GAP proteins that mediate
RT clathrin-dependent trafficking of vacuolar cargo from the trans-Golgi
RT network.";
RL Plant Cell 25:2217-2235(2013).
RN [16]
RP FUNCTION, DISRUPTION PHENOTYPE, AND REVIEW.
RX PubMed=25763490; DOI=10.4161/psb.29115;
RA Gubert C.M., Liljegren S.J.;
RT "HAESA and HAESA-LIKE2 activate organ abscission downstream of NEVERSHED
RT and EVERSHED in Arabidopsis flowers.";
RL Plant Signal. Behav. 9:E29115-E29115(2014).
CC -!- FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor
CC (ARF) (PubMed:19429787). Mediates clathrin-dependent trafficking of
CC vacuolar cargo from the trans-Golgi network (TGN) (PubMed:23771894).
CC Promotes plant growth (PubMed:23771894, PubMed:25763490). Involved in
CC the regulation of membrane trafficking and cell separation during
CC floral organ shedding and abscission (PubMed:19429787, PubMed:20081191,
CC PubMed:20230490, PubMed:23963677). Prevents abscission zone (AZ) cells
CC enlargement (PubMed:23963677, PubMed:25763490). Exhibits ARF-GTPase
CC activity toward ARF1 at TGN (PubMed:21105926).
CC {ECO:0000269|PubMed:19429787, ECO:0000269|PubMed:20081191,
CC ECO:0000269|PubMed:20230490, ECO:0000269|PubMed:21105926,
CC ECO:0000269|PubMed:23771894, ECO:0000269|PubMed:23963677,
CC ECO:0000269|PubMed:25763490}.
CC -!- SUBUNIT: Interacts with ARF1 at trans-Golgi network (TGN)
CC (PubMed:21105926). Binds to clathrin heavy chain (PubMed:23771894).
CC {ECO:0000269|PubMed:21105926, ECO:0000269|PubMed:23771894}.
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network
CC {ECO:0000269|PubMed:19429787, ECO:0000269|PubMed:21105926,
CC ECO:0000269|PubMed:23771894}. Endosome {ECO:0000269|PubMed:19429787}.
CC Cytoplasmic vesicle, clathrin-coated vesicle
CC {ECO:0000269|PubMed:23771894}. Note=Colocalizes with AGD5 at the trans-
CC Golgi network (TGN) (PubMed:21105926). Colocalizes with clathrin at the
CC TGN (PubMed:23771894). {ECO:0000269|PubMed:21105926,
CC ECO:0000269|PubMed:23771894}.
CC -!- TISSUE SPECIFICITY: Expressed in inflorescence stems, abscission zones,
CC stigmas, roots, roots meristems, embryos, and floral and leaf
CC vasculatures. {ECO:0000269|PubMed:19429787,
CC ECO:0000269|PubMed:23771894}.
CC -!- DEVELOPMENTAL STAGE: Strongly expressed in developing and mature
CC embryos. {ECO:0000269|PubMed:23771894}.
CC -!- DISRUPTION PHENOTYPE: Abnormal vacuolar trafficking of soluble cargo
CC proteins, and premature termination of the shoot apical meristem and of
CC floral meristems leading to short siliques and abscission defect
CC (PubMed:23771894, PubMed:25763490). Plant missing both AGD5 and MTV1
CC are severely dwarfed and have altered subcellular distribution of
CC clathrin-coated vesicle (CCV) cargo exported from the trans-Golgi
CC network (TGN) (PubMed:23771894). Floral organs remain attached to the
CC plant body after the shedding of mature seeds, including abnormal petal
CC breakstrength (pBS) (PubMed:23963677, PubMed:19429787, PubMed:20081191,
CC PubMed:20230490). Ectopic enlargement of abscission zone (AZ) cells
CC during shedding (PubMed:23963677). Impaired floral organ shedding
CC associated with defects in the structure of the Golgi apparatus and
CC extensive accumulation of vesicles adjacent to the cell walls in
CC abscission zone regions (PubMed:19429787, PubMed:20081191,
CC PubMed:20230490). Rescued by SOBIR1/EVR disruption, leading to
CC premature shedding of floral organs and enlarge abscission zones
CC (PubMed:20081191). Rescued by SERK1 disruption, leading to normal Golgi
CC apparatus and endosome, as well as correct floral organ shedding
CC (PubMed:20230490). {ECO:0000269|PubMed:19429787,
CC ECO:0000269|PubMed:20081191, ECO:0000269|PubMed:20230490,
CC ECO:0000269|PubMed:23771894, ECO:0000269|PubMed:23963677,
CC ECO:0000269|PubMed:25763490}.
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DR EMBL; FJ794601; ACQ91177.1; -; mRNA.
DR EMBL; AB010695; BAB10754.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96483.1; -; Genomic_DNA.
DR EMBL; AY099716; AAM20567.1; -; mRNA.
DR EMBL; BT000287; AAN15606.1; -; mRNA.
DR EMBL; AY088913; AAM67219.1; -; mRNA.
DR EMBL; AK226402; BAE98548.1; -; mRNA.
DR EMBL; AF184144; AAG17004.1; -; mRNA.
DR RefSeq; NP_568807.1; NM_124811.5.
DR AlphaFoldDB; Q9FL69; -.
DR SMR; Q9FL69; -.
DR BioGRID; 20763; 3.
DR STRING; 3702.AT5G54310.1; -.
DR iPTMnet; Q9FL69; -.
DR MetOSite; Q9FL69; -.
DR PaxDb; Q9FL69; -.
DR PRIDE; Q9FL69; -.
DR ProteomicsDB; 244742; -.
DR EnsemblPlants; AT5G54310.1; AT5G54310.1; AT5G54310.
DR GeneID; 835519; -.
DR Gramene; AT5G54310.1; AT5G54310.1; AT5G54310.
DR KEGG; ath:AT5G54310; -.
DR Araport; AT5G54310; -.
DR TAIR; locus:2162580; AT5G54310.
DR eggNOG; KOG0703; Eukaryota.
DR HOGENOM; CLU_030143_0_0_1; -.
DR InParanoid; Q9FL69; -.
DR OMA; RSSFEQH; -.
DR OrthoDB; 1097163at2759; -.
DR PhylomeDB; Q9FL69; -.
DR PRO; PR:Q9FL69; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FL69; baseline and differential.
DR Genevisible; Q9FL69; AT.
DR GO; GO:0030136; C:clathrin-coated vesicle; IDA:UniProtKB.
DR GO; GO:0005768; C:endosome; IDA:TAIR.
DR GO; GO:0005802; C:trans-Golgi network; IDA:UniProtKB.
DR GO; GO:0030276; F:clathrin binding; IDA:UniProtKB.
DR GO; GO:0005096; F:GTPase activator activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0090630; P:activation of GTPase activity; IDA:TAIR.
DR GO; GO:0035652; P:clathrin-coated vesicle cargo loading; IMP:UniProtKB.
DR GO; GO:0050829; P:defense response to Gram-negative bacterium; IMP:TAIR.
DR GO; GO:0010227; P:floral organ abscission; IMP:UniProtKB.
DR GO; GO:0060866; P:leaf abscission; IMP:TAIR.
DR GO; GO:0030308; P:negative regulation of cell growth; IMP:UniProtKB.
DR GO; GO:0060858; P:vesicle-mediated transport involved in floral organ abscission; IMP:UniProtKB.
DR Gene3D; 1.10.220.150; -; 1.
DR InterPro; IPR044520; ARF_GAP_AGD5/15.
DR InterPro; IPR037278; ARFGAP/RecO.
DR InterPro; IPR001164; ArfGAP_dom.
DR InterPro; IPR038508; ArfGAP_dom_sf.
DR PANTHER; PTHR46419; PTHR46419; 1.
DR Pfam; PF01412; ArfGap; 1.
DR PRINTS; PR00405; REVINTRACTNG.
DR SMART; SM00105; ArfGap; 1.
DR SUPFAM; SSF57863; SSF57863; 1.
DR PROSITE; PS50115; ARFGAP; 1.
PE 1: Evidence at protein level;
KW Cytoplasmic vesicle; Endosome; Golgi apparatus; GTPase activation;
KW Metal-binding; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..483
FT /note="ADP-ribosylation factor GTPase-activating protein
FT AGD5"
FT /id="PRO_0000352497"
FT DOMAIN 16..130
FT /note="Arf-GAP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00288"
FT ZN_FING 31..54
FT /note="C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00288"
FT REGION 123..226
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 238..310
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 434..483
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 123..148
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 238..272
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 282..310
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 434..471
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 34
FT /note="C->Y: In nev-9; impaired floral organ shedding."
FT /evidence="ECO:0000269|PubMed:19429787"
FT MUTAGEN 51
FT /note="C->Y: In nev-1; impaired floral organ shedding."
FT /evidence="ECO:0000269|PubMed:19429787"
FT MUTAGEN 59
FT /note="R->K: In nev-3; impaired floral organ shedding."
FT /evidence="ECO:0000269|PubMed:19429787"
FT MUTAGEN 59
FT /note="R->Q: Impaired ARF-GTPase activity toward ARF1 at
FT trans-Golgi network."
FT /evidence="ECO:0000269|PubMed:21105926"
FT CONFLICT 145
FT /note="R -> T (in Ref. 5; AAM67219)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 483 AA; 52593 MW; 7698FA235CCB50B4 CRC64;
MNEKANVSKE LNARHRKILE GLLKHPENRE CADCKTKGPR WASVNLGIFI CMQCSGIHRS
LGVHISKVRS ATLDTWLPEQ VAFIQSMGND KANSYWEAEL PPNYDRVGIE NFIRAKYEEK
RWVSRGEKAR SPPRVEQERR KSVERSGPGY EHGHSSSPVN LFEERKTIPA SRTRNNVAAT
RINLPVPPQG PSQVIKPQQK MESAATPVER EKQAVNVAPA SDPPKVDFAT DLFNMLSMDD
STTNTSEATP GDTPADDNSW AGFQSAGSGQ TAEKIVTAKP AESSSPPASS SDFEDLFKDT
PNLTTQQAPK DVKGDIMSLF EKTNIVSPFA MHQQQVAMLA QQQALYMAAA KAAGGTPNGV
NQQAIANALN VASANWSNPG GYQIPGMTNP VGGQADLQKL MQNMNMNANM NTRPAQPQEN
TLQYPSSSFY TMGQANQVNG MTPNSTGKPQ SSSATQPTST TPSSQSGKDF DFSSLMDGMF
TKH
