PRT6_ARATH
ID PRT6_ARATH Reviewed; 2006 AA.
AC F4KCC2; Q96248; Q9LZ94; Q9LZ95;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 72.
DE RecName: Full=E3 ubiquitin-protein ligase PRT6 {ECO:0000305};
DE EC=2.3.2.27;
DE AltName: Full=Protein GREENING AFTER EXTENDED DARKNESS 1 {ECO:0000303|PubMed:25667318};
DE AltName: Full=Protein PROTEOLYSIS 6 {ECO:0000303|PubMed:17572409};
DE AltName: Full=RING-type E3 ubiquitin transferase PRT6 {ECO:0000305};
GN Name=PRT6 {ECO:0000303|PubMed:17572409};
GN Synonyms=CER3 {ECO:0000303|PubMed:8811860},
GN GED1 {ECO:0000303|PubMed:25667318};
GN OrderedLocusNames=At5g02310/At5g02300 {ECO:0000312|Araport:AT5G02310};
GN ORFNames=T1E22.70/T1E22.60 {ECO:0000312|EMBL:CAB85535.1,
GN ECO:0000312|EMBL:CAB85536.1};
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 [MRNA] OF 1225-2006.
RC STRAIN=cv. Wassilewskija;
RX PubMed=8811860; DOI=10.1046/j.1365-313x.1996.10030459.x;
RA Hannoufa A., Negruk V., Eisner G., Lemieux B.;
RT "The CER3 gene of Arabidopsis thaliana is expressed in leaves, stems,
RT roots, flowers and apical meristems.";
RL Plant J. 10:459-467(1996).
RN [4]
RP FUNCTION.
RX PubMed=17572409; DOI=10.1016/j.febslet.2007.06.005;
RA Garzon M., Eifler K., Faust A., Scheel H., Hofmann K., Koncz C.,
RA Yephremov A., Bachmair A.;
RT "PRT6/At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule
RT pathway with arginine specificity and is not the CER3 locus.";
RL FEBS Lett. 581:3189-3196(2007).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=19255443; DOI=10.1073/pnas.0810280106;
RA Holman T.J., Jones P.D., Russell L., Medhurst A., Ubeda Tomas S.,
RA Talloji P., Marquez J., Schmuths H., Tung S.A., Taylor I., Footitt S.,
RA Bachmair A., Theodoulou F.L., Holdsworth M.J.;
RT "The N-end rule pathway promotes seed germination and establishment through
RT removal of ABA sensitivity in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:4549-4554(2009).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19620738; DOI=10.1073/pnas.0906404106;
RA Graciet E., Walter F., O'Maoileidigh D.S., Pollmann S., Meyerowitz E.M.,
RA Varshavsky A., Wellmer F.;
RT "The N-end rule pathway controls multiple functions during Arabidopsis
RT shoot and leaf development.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:13618-13623(2009).
RN [7]
RP FUNCTION.
RX PubMed=22020282; DOI=10.1038/nature10536;
RA Licausi F., Kosmacz M., Weits D.A., Giuntoli B., Giorgi F.M.,
RA Voesenek L.A., Perata P., van Dongen J.T.;
RT "Oxygen sensing in plants is mediated by an N-end rule pathway for protein
RT destabilization.";
RL Nature 479:419-422(2011).
RN [8]
RP DISRUPTION PHENOTYPE.
RX PubMed=25667318; DOI=10.1104/pp.114.253088;
RA Riber W., Mueller J.T., Visser E.J., Sasidharan R., Voesenek L.A.,
RA Mustroph A.;
RT "The greening after extended darkness1 is an N-end rule pathway mutant with
RT high tolerance to submergence and starvation.";
RL Plant Physiol. 167:1616-1629(2015).
RN [9]
RP FUNCTION.
RX PubMed=27173012; DOI=10.1038/srep26020;
RA de Marchi R., Sorel M., Mooney B., Fudal I., Goslin K., Kwasniewska K.,
RA Ryan P.T., Pfalz M., Kroymann J., Pollmann S., Feechan A., Wellmer F.,
RA Rivas S., Graciet E.;
RT "The N-end rule pathway regulates pathogen responses in plants.";
RL Sci. Rep. 6:26020-26020(2016).
RN [10]
RP FUNCTION.
RX PubMed=29168982; DOI=10.1111/nph.14909;
RA Zhang H., Gannon L., Hassall K.L., Deery M.J., Gibbs D.J., Holdsworth M.J.,
RA van der Hoorn R.A.L., Lilley K.S., Theodoulou F.L.;
RT "N-terminomics reveals control of Arabidopsis seed storage proteins and
RT proteases by the Arg/N-end rule pathway.";
RL New Phytol. 218:1106-1126(2018).
RN [11]
RP FUNCTION.
RX PubMed=30117535; DOI=10.1111/nph.15387;
RA Vicente J., Mendiondo G.M., Pauwels J., Pastor V., Izquierdo Y.,
RA Naumann C., Movahedi M., Rooney D., Gibbs D.J., Smart K., Bachmair A.,
RA Gray J.E., Dissmeyer N., Castresana C., Ray R.V., Gevaert K.,
RA Holdsworth M.J.;
RT "Distinct branches of the N-end rule pathway modulate the plant immune
RT response.";
RL New Phytol. 221:988-1000(2019).
CC -!- FUNCTION: Ubiquitin protein ligase which is a component of the N-end
CC rule pathway with arginine specificity, and functions with the
CC arginyltransferases ATE1 and ATE2. Recognizes and binds to proteins
CC bearing specific N-terminal residues that are destabilizing according
CC to the N-end rule, leading to their ubiquitination and subsequent
CC degradation (PubMed:17572409, PubMed:19255443, PubMed:19620738,
CC PubMed:22020282). Does not participate in degradation of proteins with
CC N-terminal Phe or Leu (PubMed:17572409). The N-end rule pathway
CC regulates seed after-ripening, seedling sugar sensitivity, seedling
CC lipid breakdown, and abscisic acid (ABA) sensitivity of germination
CC (PubMed:19255443). The N-end rule pathway regulates various aspects of
CC leaf and shoot development (PubMed:19620738). Involved in the
CC ubiquitination and subsequent degradation of RAP2-12, an activator of
CC hypoxic gene expression. The ubiquitination occurs after the N-
CC arginylation of RAP2-12 by ATE1 or ATE2 under aerobic conditions
CC (PubMed:22020282). The end-rule pathway plays a role in regulating the
CC timing and amplitude of the immune response following infection with
CC the bacterial pathogen Pseudomonas syringae pv tomato (PubMed:27173012,
CC PubMed:30117535). Regulates the biosynthesis of plant-defense
CC metabolites such as glucosinolates, and the biosynthesis and response
CC to the phytohormone jasmonate (JA), which plays a key role in plant
CC immunity (PubMed:27173012). Controls the expression of specific
CC defense-response genes, activates the synthesis pathway for the
CC phytoalexin camalexin, and influences basal resistance to the
CC hemibiotroph pathogen Pseudomonas syringae pv tomato (PubMed:30117535).
CC Coordinates the mobilization of seed storage reserves and regulates the
CC abundance and activities of several proteases following seed
CC germination (PubMed:29168982). {ECO:0000269|PubMed:17572409,
CC ECO:0000269|PubMed:19255443, ECO:0000269|PubMed:19620738,
CC ECO:0000269|PubMed:22020282, ECO:0000269|PubMed:27173012,
CC ECO:0000269|PubMed:29168982, ECO:0000269|PubMed:30117535}.
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;
CC -!- PATHWAY: Protein modification; protein ubiquitination. {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Reduced seed germination potential and inhibition
CC of seedling establishment by sucrose (PubMed:19255443). Exhibits
CC abnormal shoot and leaf development (PubMed:19620738). Increased
CC tolerance of seedlings to submergence and starvation (PubMed:25667318).
CC {ECO:0000269|PubMed:19255443, ECO:0000269|PubMed:19620738,
CC ECO:0000269|PubMed:25667318}.
CC -!- SIMILARITY: Belongs to the UBR1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB85535.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At5g02300 and At5g02310.; Evidence={ECO:0000305};
CC Sequence=CAB85536.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At5g02300 and At5g02310.; Evidence={ECO:0000305};
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DR EMBL; AL162874; CAB85535.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL162874; CAB85536.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED90457.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM70335.1; -; Genomic_DNA.
DR EMBL; X95962; CAA65198.1; -; Genomic_DNA.
DR PIR; T48251; T48251.
DR PIR; T48252; T48252.
DR RefSeq; NP_001318457.1; NM_001342651.1.
DR RefSeq; NP_195851.2; NM_120309.2.
DR PDB; 6LHN; X-ray; 2.50 A; A=119-189.
DR PDBsum; 6LHN; -.
DR AlphaFoldDB; F4KCC2; -.
DR SMR; F4KCC2; -.
DR STRING; 3702.AT5G02310.1; -.
DR iPTMnet; F4KCC2; -.
DR PaxDb; F4KCC2; -.
DR PRIDE; F4KCC2; -.
DR ProteomicsDB; 226480; -.
DR EnsemblPlants; AT5G02310.1; AT5G02310.1; AT5G02310.
DR EnsemblPlants; AT5G02310.3; AT5G02310.3; AT5G02310.
DR GeneID; 830916; -.
DR Gramene; AT5G02310.1; AT5G02310.1; AT5G02310.
DR Gramene; AT5G02310.3; AT5G02310.3; AT5G02310.
DR KEGG; ath:AT5G02310; -.
DR Araport; AT5G02310; -.
DR TAIR; locus:2180147; AT5G02310.
DR eggNOG; KOG1139; Eukaryota.
DR eggNOG; KOG1140; Eukaryota.
DR HOGENOM; CLU_001801_1_0_1; -.
DR InParanoid; F4KCC2; -.
DR OrthoDB; 81415at2759; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:F4KCC2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4KCC2; baseline and differential.
DR Genevisible; F4KCC2; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0000151; C:ubiquitin ligase complex; IBA:GO_Central.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0042742; P:defense response to bacterium; IMP:TAIR.
DR GO; GO:0050832; P:defense response to fungus; IMP:TAIR.
DR GO; GO:0016567; P:protein ubiquitination; IBA:GO_Central.
DR GO; GO:0050994; P:regulation of lipid catabolic process; IMP:TAIR.
DR GO; GO:0010029; P:regulation of seed germination; IMP:TAIR.
DR GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IDA:TAIR.
DR GO; GO:0071596; P:ubiquitin-dependent protein catabolic process via the N-end rule pathway; IBA:GO_Central.
DR Gene3D; 1.10.10.2670; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR042065; E3_ELL-like.
DR InterPro; IPR044046; E3_ligase_UBR-like_C.
DR InterPro; IPR039164; UBR1-like.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR003126; Znf_UBR.
DR PANTHER; PTHR21497; PTHR21497; 1.
DR Pfam; PF18995; PRT6_C; 1.
DR Pfam; PF02207; zf-UBR; 1.
DR SMART; SM00396; ZnF_UBR1; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR PROSITE; PS51157; ZF_UBR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Metal-binding; Plant defense; Reference proteome;
KW Transferase; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..2006
FT /note="E3 ubiquitin-protein ligase PRT6"
FT /id="PRO_0000431720"
FT ZN_FING 119..189
FT /note="UBR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00508"
FT ZN_FING 1395..1440
FT /note="RING-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 1167..1186
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1338..1380
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1172..1186
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1350..1366
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 1341
FT /note="P -> H (in Ref. 3; CAA65198)"
FT /evidence="ECO:0000305"
FT CONFLICT 1430
FT /note="Missing (in Ref. 3; CAA65198)"
FT /evidence="ECO:0000305"
FT CONFLICT 1838
FT /note="L -> F (in Ref. 3; CAA65198)"
FT /evidence="ECO:0000305"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:6LHN"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:6LHN"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:6LHN"
FT HELIX 147..151
FT /evidence="ECO:0007829|PDB:6LHN"
FT STRAND 160..169
FT /evidence="ECO:0007829|PDB:6LHN"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:6LHN"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:6LHN"
FT HELIX 185..187
FT /evidence="ECO:0007829|PDB:6LHN"
SQ SEQUENCE 2006 AA; 223964 MW; 77B373F169C77DCC CRC64;
METNSSLFGL VSPSSHDLVI ERLASVGVPK KYRSKRGLVE FVRANPAKIS ELVSALLPTD
DDVKLGLKEA RERPRKSAVS PTMKKRFRES MNMLQWLMFQ DEPDVSLRNL AKLNLDQRGV
CGSVWGQNDI AYRCRTCEND PTCAICVPCF QNGDHNSHDY SIIYTGGGCC DCGDETAWKP
DGFCSNHKGS EQIRPLSENL ANSVGPILDA LFTCWNNKLL SAESSGQKGA RSNDTLVILQ
KMSNELTFIV VEMLLEFSMS SESLLSFVSR RIISSSGLLS ILLKAERFLD QDVMKKLHDL
FLKLIGDPVF KCEFAKAFVS YYPVVISEVV KQGTDNAFKK YPLLSTFSVQ ILTVPTLTPF
LVKEMNLLAM LLGCLSDIFV SCSGEDGLLQ ATKLERLCET SERVIGDLKF VMSHAIVSKY
ATHEHRELSR SWLTLLTFAQ GMNPLKRETG IPIDEENDYM HLFFVLGHSI AVIHSLLVNG
TYSAASDEEI ENDRNAKEEF DKCDGDGERY AKVGRLSHED SVCTAIVSSS SFDSSMASEV
HKIDPFHALL PSSAIYLIRE CLKVLETCLG NDEGISKFLC KLSSSSGRNI PESKMSWPRR
DLLNVETGGS VSSNLASSSR DPSTGLSPLC GDIQTNLSLD NVCGPYGVVQ TDVTADSKRV
SCNSADLTKN ASGLRILGLC DWPDIHYDVS SQAISVHLPL HRLLSLLIQK ALRICYGESA
SYNGVSISHE IPHADFFSSV IGDFHPCGFS ALVMEHVLQI RVFCAQVIAG MWKKNGDSAL
VSCEWYRSVR WSEQGLELDL FLLQCCAALA PADSYVDKLL SRFGLSSYLS LNPDITNEYE
PVLVQEMLGL LIQILQERRF CGLSTAESLR REIIFKLATG DFTHSQLVKS LPRDLSKSDE
LQEVLDDVSV YCNPSGMNQG KYSLQSSCWK ELDLYHPRWQ SRDLQSAEER FSRYCGVSAL
TTQLPRWRMI YPPLKGLARI GTCKATFQII SSALYYALQS GTSVKSRAPD GVLITALQLL
SLSLDICTQQ RQSNSQDCCL ENSIPILELA GLEIIGIAQG TEKESLLSLL VSLMKTRMGD
GRHQFPEPGS CNISSWIGNL LKKFSAIDSV CMNLLQSLAP EVVGQSGFDK VMSGSTSDEK
RKAKAKERQA AIMAKMKAEQ SKFLSTLSSS MDDDDPRSEF ETSDSVMEHD SEIAVREVCS
LCHDPDSKDP VSFLIFLQKS KLLSFVDRGP PSWDQCPQSE KKISVDGAPD LLRMNASSDS
LRISSPLMLQ LSDDTISESA NMIESIKARL IGNGQTEKRS SDGRGKDESN MESLEIAMYQ
TVRNKIENMI NQSLTRVDHQ PHEAENCSEK NSVGGPSTLQ GRFPDIRSRQ TSRRPDAGSD
GFHPIDCDGV YLSSCGHAVH QSCLERYLKS LKERSGRRTV FEGAHIVDLK KKEFLCPVCR
RLANSVLPEC PGDLCSVSKL QDSPRTKLRR KDALQPSLWL SEALCLLRSA AEVIEDGDRG
KTVTPQGDGP RRKDLKSVSK MLWDFYFPKP EDKTLKRLWL PPQSIVMWDT LKYSLISMEI
GTRFAKNSML PVYCIDSLYE ELKTSKGTIL SVLLRVVQSS RTKNTIHVRQ RFVGMKHLAE
SICYGVSSSS SSSIFGSEGT TGSLKNIDLL WNRASDPVLA HDPFSSLMWA LFCLPFPFLT
CEESLLSLVH IFHSVSLVQT VIAYCACRPS ELSELNFGEN LLNDISNALR ESGGWEYFRS
NNMDLSCDIK DTIRKYSLPF LRRCALLWKL LKSTPRKLHE ESDMFDLPSD PTTDNMDFIY
SPQSELNHVQ ELEKMFNIPP IDIILNDELL RSSTQIWLQH FQREYRVNRV KRSLCITPVV
PFQLMKLPNL YQDLLQRCIK KRCVNCTKVI EEPVLCLLCG SLCSPIWSPC CRESGCPNHA
ITCGAGTGVF LLIRRTTILL QRFARQSPWP SPYLDTFGEE DIDMIRGKRL YLNEERYAAL
TYLVGSHGLD RSSKVLGQTT IGAVLH
