AGD3_ARATH
ID AGD3_ARATH Reviewed; 827 AA.
AC Q5W7F2; Q0WNK6; Q9LYU6;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=ADP-ribosylation factor GTPase-activating protein AGD3;
DE Short=ARF GAP AGD3;
DE AltName: Full=Protein ARF-GAP DOMAIN 3;
DE Short=AtAGD3;
DE AltName: Full=Protein FORKED 2 {ECO:0000303|PubMed:19363154, ECO:0000303|PubMed:19473324};
DE AltName: Full=Protein SCARFACE;
DE AltName: Full=Protein VASCULAR NETWORK 3 {ECO:0000303|PubMed:19363154};
GN Name=AGD3;
GN Synonyms=FKD2 {ECO:0000303|PubMed:19363154, ECO:0000303|PubMed:19473324},
GN SFC, VAN3 {ECO:0000303|PubMed:19363154};
GN OrderedLocusNames=At5g13300 {ECO:0000312|Araport:AT5G13300};
GN ORFNames=T31B5.120 {ECO:0000312|EMBL:CAB86637.1};
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], INDUCTION BY AUXIN, SUBUNIT, SUBCELLULAR
RP LOCATION, AND FUNCTION.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=15743878; DOI=10.1242/dev.01716;
RA Koizumi K., Naramoto S., Sawa S., Yahara N., Ueda T., Nakano A.,
RA Sugiyama M., Fukuda H.;
RT "VAN3 ARF-GAP-mediated vesicle transport is involved in leaf vascular
RT network formation.";
RL Development 132:1699-1711(2005).
RN [2]
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 [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] OF 419-827.
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.
RX PubMed=10887076; DOI=10.1242/dev.127.15.3197;
RA Koizumi K., Sugiyama M., Fukuda H.;
RT "A series of novel mutants of Arabidopsis thaliana that are defective in
RT the formation of continuous vascular network: calling the auxin signal flow
RT canalization hypothesis into question.";
RL Development 127:3197-3204(2000).
RN [6]
RP FUNCTION.
RX PubMed=10887077; DOI=10.1242/dev.127.15.3205;
RA Deyholos M.K., Cordner G., Beebe D., Sieburth L.E.;
RT "The SCARFACE gene is required for cotyledon and leaf vein patterning.";
RL Development 127:3205-3213(2000).
RN [7]
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 [8]
RP INTERACTION WITH DRP1A.
RX PubMed=15923323; DOI=10.1104/pp.105.061689;
RA Sawa S., Koizumi K., Naramoto S., Demura T., Ueda T., Nakano A., Fukuda H.;
RT "DRP1A is responsible for vascular continuity synergistically working with
RT VAN3 in Arabidopsis.";
RL Plant Physiol. 138:819-826(2005).
RN [9]
RP FUNCTION, TISSUE SPECIFICITY, AND MUTAGENESIS OF ASP-518 AND CYS-519.
RX PubMed=16698946; DOI=10.1105/tpc.105.039008;
RA Sieburth L.E., Muday G.K., King E.J., Benton G., Kim S., Metcalf K.E.,
RA Meyers L., Seamen E., Van Norman J.M.;
RT "SCARFACE encodes an ARF-GAP that is required for normal auxin efflux and
RT vein patterning in Arabidopsis.";
RL Plant Cell 18:1396-1411(2006).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-445, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [11]
RP MUTAGENESIS OF GLY-321, SUBCELLULAR LOCATION, INTERACTION WITH VAB, AND
RP ACTIVITY REGULATION.
RX PubMed=19363154; DOI=10.1242/dev.030098;
RA Naramoto S., Sawa S., Koizumi K., Uemura T., Ueda T., Friml J., Nakano A.,
RA Fukuda H.;
RT "Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and
RT activity essential for vascular tissue continuity in plants.";
RL Development 136:1529-1538(2009).
RN [12]
RP MUTAGENESIS OF LEU-317 AND GLY-321, TISSUE SPECIFICITY, DEVELOPMENTAL
RP STAGE, AND PH DOMAIN.
RX PubMed=19473324; DOI=10.1111/j.1365-313x.2009.03920.x;
RA Carland F., Nelson T.;
RT "CVP2- and CVL1-mediated phosphoinositide signaling as a regulator of the
RT ARF GAP SFC/VAN3 in establishment of foliar vein patterns.";
RL Plant J. 59:895-907(2009).
CC -!- FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor
CC (ARF). Involved in the spatial control of provascular differentiation.
CC Required for the formation of the normal pattern of continuous
CC secondary veins. Involved in auxin signaling but not in polar auxin
CC transport or in auxin responses. Required for PIN1 internalization in
CC roots. {ECO:0000269|PubMed:10887076, ECO:0000269|PubMed:10887077,
CC ECO:0000269|PubMed:15743878, ECO:0000269|PubMed:16698946}.
CC -!- ACTIVITY REGULATION: ARF GAP activity strongly enhanced by
CC phosphatidylinositol 4-monophosphate (PIP) and moderately enhanced by
CC phosphatidylinositol 4,5-bisphosphate (PIP2).
CC {ECO:0000269|PubMed:19363154}.
CC -!- SUBUNIT: Homodimer (PubMed:15743878). Interacts with DRP1A
CC (PubMed:15923323). Interacts with VAB (PubMed:19363154).
CC {ECO:0000269|PubMed:15743878, ECO:0000269|PubMed:15923323,
CC ECO:0000269|PubMed:19363154}.
CC -!- INTERACTION:
CC Q5W7F2; P42697: DRP1A; NbExp=4; IntAct=EBI-994222, EBI-994234;
CC Q5W7F2; Q8W4K5: VAB; NbExp=5; IntAct=EBI-994222, EBI-10769249;
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network
CC {ECO:0000269|PubMed:15743878, ECO:0000269|PubMed:19363154}. Note=BAR
CC and PH domains are essential for the proper localization. Localization
CC seems to be regulated by CVP2 and CVL1 activity as the
CC phosphatidylinositol 4-monophosphate (PIP)-binding by the PH domain is
CC required for the TGN localization. {ECO:0000269|PubMed:19363154}.
CC -!- TISSUE SPECIFICITY: Broadly expressed. Detected in developing veins of
CC the leaf and root (PubMed:19473324). Detected in roots, hypocotyls,
CC cotyledons, leaves, siliques and shoot apical meristems
CC (PubMed:16698946). {ECO:0000269|PubMed:16698946,
CC ECO:0000269|PubMed:19473324}.
CC -!- DEVELOPMENTAL STAGE: Expression refined to procambial cells during
CC embryogenesis. {ECO:0000269|PubMed:19473324}.
CC -!- INDUCTION: Up-regulated by auxin. {ECO:0000269|PubMed:15743878}.
CC -!- DOMAIN: The PH domain is responsive of the binding to phosphoinositol
CC (PubMed:19473324). The BAR domain is required and sufficient for
CC homodimerization (PubMed:15743878). {ECO:0000269|PubMed:15743878,
CC ECO:0000269|PubMed:19473324}.
CC -!- MISCELLANEOUS: Binds to phosphatidylinositol (PI), phosphatidylinositol
CC 4-monophosphate (PIP) and phosphatidylinositol 4,5-bisphosphate (PIP2)
CC but not to phosphatidic acid (PA), phosphatidylcholine (PC) or
CC phosphatidylethanolamine (PE). {ECO:0000269|PubMed:15743878}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB86637.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL163491; CAB86637.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91878.1; -; Genomic_DNA.
DR EMBL; AB194395; BAD69588.1; -; mRNA.
DR EMBL; AK229433; BAF01293.1; -; mRNA.
DR PIR; T48577; T48577.
DR RefSeq; NP_196834.3; NM_121333.4.
DR AlphaFoldDB; Q5W7F2; -.
DR SMR; Q5W7F2; -.
DR BioGRID; 16449; 4.
DR IntAct; Q5W7F2; 3.
DR STRING; 3702.AT5G13300.1; -.
DR iPTMnet; Q5W7F2; -.
DR PaxDb; Q5W7F2; -.
DR PRIDE; Q5W7F2; -.
DR ProteomicsDB; 243286; -.
DR EnsemblPlants; AT5G13300.1; AT5G13300.1; AT5G13300.
DR GeneID; 831171; -.
DR Gramene; AT5G13300.1; AT5G13300.1; AT5G13300.
DR KEGG; ath:AT5G13300; -.
DR Araport; AT5G13300; -.
DR TAIR; locus:2183916; AT5G13300.
DR eggNOG; KOG0521; Eukaryota.
DR HOGENOM; CLU_016029_1_0_1; -.
DR InParanoid; Q5W7F2; -.
DR OMA; QATYFQQ; -.
DR OrthoDB; 751525at2759; -.
DR PhylomeDB; Q5W7F2; -.
DR PRO; PR:Q5W7F2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q5W7F2; baseline and differential.
DR Genevisible; Q5W7F2; AT.
DR GO; GO:0005794; C:Golgi apparatus; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IDA:TAIR.
DR GO; GO:0030140; C:trans-Golgi network transport vesicle; IDA:UniProtKB.
DR GO; GO:0005096; F:GTPase activator activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035091; F:phosphatidylinositol binding; IDA:TAIR.
DR GO; GO:0006897; P:endocytosis; IMP:TAIR.
DR GO; GO:0009965; P:leaf morphogenesis; IMP:TAIR.
DR GO; GO:0010087; P:phloem or xylem histogenesis; IMP:TAIR.
DR GO; GO:0009733; P:response to auxin; IMP:TAIR.
DR GO; GO:0010051; P:xylem and phloem pattern formation; IMP:TAIR.
DR CDD; cd07606; BAR_SFC_plant; 1.
DR Gene3D; 1.10.220.150; -; 1.
DR Gene3D; 1.20.1270.60; -; 1.
DR Gene3D; 1.25.40.20; -; 1.
DR Gene3D; 2.30.29.30; -; 1.
DR InterPro; IPR045258; ACAP1/2/3-like.
DR InterPro; IPR035670; AGD1/2/3/4_BAR_plant.
DR InterPro; IPR027267; AH/BAR_dom_sf.
DR InterPro; IPR002110; Ankyrin_rpt.
DR InterPro; IPR036770; Ankyrin_rpt-contain_sf.
DR InterPro; IPR037278; ARFGAP/RecO.
DR InterPro; IPR001164; ArfGAP_dom.
DR InterPro; IPR038508; ArfGAP_dom_sf.
DR InterPro; IPR004148; BAR_dom.
DR InterPro; IPR011993; PH-like_dom_sf.
DR InterPro; IPR001849; PH_domain.
DR PANTHER; PTHR23180; PTHR23180; 1.
DR Pfam; PF13637; Ank_4; 1.
DR Pfam; PF01412; ArfGap; 1.
DR Pfam; PF00169; PH; 1.
DR PRINTS; PR00405; REVINTRACTNG.
DR SMART; SM00248; ANK; 3.
DR SMART; SM00105; ArfGap; 1.
DR SMART; SM00721; BAR; 1.
DR SMART; SM00233; PH; 1.
DR SUPFAM; SSF103657; SSF103657; 1.
DR SUPFAM; SSF48403; SSF48403; 1.
DR SUPFAM; SSF57863; SSF57863; 1.
DR PROSITE; PS50297; ANK_REP_REGION; 1.
DR PROSITE; PS50088; ANK_REPEAT; 2.
DR PROSITE; PS50115; ARFGAP; 1.
DR PROSITE; PS50003; PH_DOMAIN; 1.
PE 1: Evidence at protein level;
KW ANK repeat; Coiled coil; Developmental protein; Golgi apparatus;
KW GTPase activation; Metal-binding; Phosphoprotein; Reference proteome;
KW Repeat; Zinc; Zinc-finger.
FT CHAIN 1..827
FT /note="ADP-ribosylation factor GTPase-activating protein
FT AGD3"
FT /id="PRO_0000332940"
FT DOMAIN 1..225
FT /note="BAR"
FT DOMAIN 292..430
FT /note="PH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00145"
FT DOMAIN 501..643
FT /note="Arf-GAP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00288"
FT REPEAT 728..757
FT /note="ANK 1"
FT REPEAT 761..790
FT /note="ANK 2"
FT REPEAT 794..825
FT /note="ANK 3"
FT ZN_FING 516..539
FT /note="C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00288"
FT REGION 246..269
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 439..467
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 116..139
FT /evidence="ECO:0000255"
FT COILED 223..253
FT /evidence="ECO:0000255"
FT COMPBIAS 253..269
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 451..465
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 445
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157"
FT MUTAGEN 317
FT /note="L->F: In fkd2-2; vein pattern defects."
FT /evidence="ECO:0000269|PubMed:19473324"
FT MUTAGEN 321
FT /note="G->E: In van3-2 and fkd2-1; reduced ARF GAP
FT activity, mis-localization and vein pattern defects."
FT /evidence="ECO:0000269|PubMed:19363154,
FT ECO:0000269|PubMed:19473324"
FT MUTAGEN 518
FT /note="D->N: In scf-6; intermediate vein pattern defects."
FT /evidence="ECO:0000269|PubMed:16698946"
FT MUTAGEN 519
FT /note="C->Y: In scf-1; strong vein pattern defects."
FT /evidence="ECO:0000269|PubMed:16698946"
SQ SEQUENCE 827 AA; 92524 MW; 59FF5BAA10584DD7 CRC64;
MHFTKLDDSP MFRKQLQSME ESAEILRERS LKFYKGCRKY TEGLGEAYDG DIAFASALET
FGGGHNDPIS VAFGGPVMTK FTIALREIGT YKEVLRSQVE HILNDRLLQF ANMDLHEVKE
ARKRFDKASL TYDQAREKFL SLRKGTKSDV AAALEQELHT SRSMFEQARF NLVTALSNVE
AKKRFEFLEA VSGTMDAHLR YFKQGYELLH QMEPYINQVL TYAQQSRERS NYEQAALNEK
MQEYKRQVDR ESRWGSNGSN GSPNGDGIQA IGRSSHKMID AVMQSAARGK VQTIRQGYLS
KRSSNLRGDW KRRFFVLDSR GMLYYYRKQC SKPSGSGSQL SGQRNSSELG SGLLSRWLSS
NNHGHGGVHD EKSVARHTVN LLTSTIKVDA DQSDLRFCFR IISPTKNYTL QAESALDQMD
WIEKITGVIA SLLSSQVPEQ RLPGSPMGSG HHRSASESSS YESSEYDHPT TEEFVCERSF
LGYNERPSRS FQPQRSIRKG EKPIDALRKV CGNDKCADCG APEPDWASLN LGVLVCIECS
GVHRNLGVHI SKVRSLTLDV KVWEPSVISL FQALGNTFAN TVWEELLHSR SAIHFDPGLT
VSDKSRVMVT GKPSYADMIS IKEKYIQAKY AEKLFVRRSR DSDFPQSAAQ QMWDAVSGND
KKAVYRLIVN GDADVNYVYD QTSSSSLTLS RVILVPERPK REDVLLRLRN ELLDRTGSSS
NISPEGSGGS SLLHCACEKA DLGMVELLLQ YGANVNASDS SGQTPLHCCL LRGKVTIARL
LLTRGADPEA MNREGKTALD IAAESNFTDP EVLALLSDTN GYNHRQC
