VAR3_ARATH
ID VAR3_ARATH Reviewed; 758 AA.
AC Q8S9K3; Q64M74; Q9FN73;
DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 2.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=Zinc finger protein VAR3, chloroplastic {ECO:0000305};
DE AltName: Full=Organelle Zinc finger 1 {ECO:0000303|PubMed:25768119};
DE AltName: Full=Protein VARIEGATED 3 {ECO:0000303|PubMed:15340011};
DE Flags: Precursor;
GN Name=VAR3 {ECO:0000303|PubMed:15340011};
GN Synonyms=OZ1 {ECO:0000303|PubMed:25768119}; OrderedLocusNames=At5g17790;
GN ORFNames=MVA3.140, MVA3.15;
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, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, INTERACTION WITH CCD4/NCED4, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Landsberg erecta; TISSUE=Flower;
RX PubMed=15340011; DOI=10.1242/jcs.01360;
RA Naested H., Holm A., Jenkins T., Nielsen H.B., Harris C.A., Beale M.H.,
RA Andersen M., Mant A., Scheller H., Camara B., Mattsson O., Mundy J.;
RT "Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger
RT protein required for chloroplast and palisade cell development.";
RL J. Cell Sci. 117:4807-4818(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
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 FUNCTION, HOMODIMERIZATION, INTERACTION WITH ORRM1, INTERACTION WITH
RP PCMP-H51/CRR28 AND PCMP-H12/OTP82, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=25768119; DOI=10.1371/journal.pgen.1005028;
RA Sun T., Shi X., Friso G., Van Wijk K., Bentolila S., Hanson M.R.;
RT "A zinc finger motif-containing protein is essential for chloroplast RNA
RT editing.";
RL PLoS Genet. 11:E1005028-E1005028(2015).
RN [6]
RP INTERACTION WITH ORRM6, AND SUBCELLULAR LOCATION.
RX PubMed=28213559; DOI=10.1104/pp.16.01623;
RA Hackett J.B., Shi X., Kobylarz A.T., Lucas M.K., Wessendorf R.L.,
RA Hines K.M., Bentolila S., Hanson M.R., Lu Y.;
RT "An organelle RNA recognition motif protein is required for photosynthetic
RT subunit psbF transcript editing.";
RL Plant Physiol. 173:2278-2293(2017).
CC -!- FUNCTION: Probable component of some protein complex required for
CC chloroplast and palisade cell development (PubMed:15340011). Involved
CC in C-to-U editing of chloroplastic RNA. Controls a large number of
CC chloroplastic editing sites. Binds the editing recognition trans-
CC factors PCMP-H51/CRR28 and PCMP-H12/OTP82 (PubMed:25768119).
CC {ECO:0000269|PubMed:15340011, ECO:0000269|PubMed:25768119}.
CC -!- SUBUNIT: Interacts in vitro with the chloroplast-located protein
CC CCD4/NCED4 (PubMed:15340011). Homodimer. Interacts with ORRM1.
CC Interacts with PCMP-H51/CRR28 and PCMP-H12/OTP82 (PubMed:25768119).
CC Interacts with ORRM6 (PubMed:28213559). {ECO:0000269|PubMed:15340011,
CC ECO:0000269|PubMed:25768119, ECO:0000269|PubMed:28213559}.
CC -!- INTERACTION:
CC Q8S9K3; O49675: CCD4; NbExp=2; IntAct=EBI-632401, EBI-632411;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:15340011, ECO:0000269|PubMed:25768119,
CC ECO:0000269|PubMed:28213559}. Note=Localizes at punctuate loci in
CC chloroplasts. {ECO:0000269|PubMed:25768119}.
CC -!- TISSUE SPECIFICITY: Weakly expressed in leaves and roots.
CC {ECO:0000269|PubMed:15340011}.
CC -!- DISRUPTION PHENOTYPE: Defects result in variegated plants that have
CC leaves consisting of normal green and also white or yellow sectors in
CC which chloroplast development is retarded or disrupted
CC (PubMed:15340011, PubMed:25768119). Mutant plants exhibit severe
CC editing defects in chloroplastic transcripts (PubMed:25768119).
CC {ECO:0000269|PubMed:15340011, ECO:0000269|PubMed:25768119}.
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DR EMBL; AY050223; AAL09834.1; -; mRNA.
DR EMBL; AB006706; BAB09578.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92469.1; -; Genomic_DNA.
DR EMBL; AY075645; AAL77653.1; -; mRNA.
DR EMBL; BT002233; AAN72244.1; -; mRNA.
DR RefSeq; NP_197281.1; NM_121785.3.
DR AlphaFoldDB; Q8S9K3; -.
DR BioGRID; 16923; 11.
DR IntAct; Q8S9K3; 8.
DR STRING; 3702.AT5G17790.1; -.
DR iPTMnet; Q8S9K3; -.
DR PaxDb; Q8S9K3; -.
DR PRIDE; Q8S9K3; -.
DR ProteomicsDB; 228575; -.
DR EnsemblPlants; AT5G17790.1; AT5G17790.1; AT5G17790.
DR GeneID; 831647; -.
DR Gramene; AT5G17790.1; AT5G17790.1; AT5G17790.
DR KEGG; ath:AT5G17790; -.
DR Araport; AT5G17790; -.
DR TAIR; locus:2175921; AT5G17790.
DR eggNOG; KOG4198; Eukaryota.
DR HOGENOM; CLU_007852_1_0_1; -.
DR InParanoid; Q8S9K3; -.
DR OMA; TEMSGDA; -.
DR OrthoDB; 571786at2759; -.
DR PhylomeDB; Q8S9K3; -.
DR PRO; PR:Q8S9K3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8S9K3; baseline and differential.
DR Genevisible; Q8S9K3; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:1900871; P:chloroplast mRNA modification; IMP:TAIR.
DR GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR InterPro; IPR001876; Znf_RanBP2.
DR InterPro; IPR036443; Znf_RanBP2_sf.
DR Pfam; PF00641; zf-RanBP; 2.
DR SMART; SM00547; ZnF_RBZ; 2.
DR SUPFAM; SSF90209; SSF90209; 1.
DR PROSITE; PS01358; ZF_RANBP2_1; 2.
DR PROSITE; PS50199; ZF_RANBP2_2; 2.
PE 1: Evidence at protein level;
KW Chloroplast; Metal-binding; mRNA processing; Plastid; Reference proteome;
KW Repeat; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..?
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN ?..758
FT /note="Zinc finger protein VAR3, chloroplastic"
FT /id="PRO_0000022653"
FT REPEAT 368..415
FT /note="1"
FT REPEAT 547..596
FT /note="2"
FT REPEAT 688..736
FT /note="3"
FT ZN_FING 276..305
FT /note="RanBP2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00322"
FT ZN_FING 308..338
FT /note="RanBP2-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00322"
FT REGION 122..502
FT /note="3 X approximate repeat"
FT REGION 410..470
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 512..545
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 572..606
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 629..654
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 727..758
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 420..459
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 523..545
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 573..598
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 632..654
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 29
FT /note="I -> V (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 52..53
FT /note="SF -> FS (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 68
FT /note="I -> L (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 73
FT /note="N -> T (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 82
FT /note="D -> E (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 89
FT /note="N -> H (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 158
FT /note="L -> M (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 168
FT /note="K -> R (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 178
FT /note="S -> G (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 185
FT /note="L -> V (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 188
FT /note="I -> L (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 191
FT /note="L -> M (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 206
FT /note="I -> L (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 214
FT /note="A -> T (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 219..224
FT /note="SKQHNK -> IKHHNQ (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 239
FT /note="A -> T (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 252
FT /note="D -> G (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 265
FT /note="G -> A (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 340
FT /note="S -> A (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 348
FT /note="D -> G (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 351
FT /note="S -> N (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 357
FT /note="R -> S (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 370
FT /note="L -> F (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 409
FT /note="P -> T (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 421
FT /note="R -> S (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 427
FT /note="N -> S (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 502
FT /note="I -> T (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 505..510
FT /note="IQVDGF -> NQIDGV (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 546
FT /note="A -> G (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 565
FT /note="I -> M (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 579
FT /note="G -> E (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 621..626
FT /note="KQPKES -> RQLKEP (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 630
FT /note="L -> I (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 637
FT /note="N -> K (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 646
FT /note="P -> A (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 649..651
FT /note="PSI -> SSS (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 655..656
FT /note="DT -> ER (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 659..660
FT /note="VK -> GM (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 666
FT /note="S -> R (in Ref. 4; AAL77653/AAN72244)"
FT /evidence="ECO:0000305"
FT CONFLICT 675
FT /note="S -> P (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
FT CONFLICT 749
FT /note="N -> D (in Ref. 1; AAL09834)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 758 AA; 85945 MW; 5659AABF750BF8DE CRC64;
MNNSTRLISL FSPHPPPLFL LRGLYISRIA NLRRFHRRAF PPSSVASTNL CSFRPLVSLP
PLIPTFPIGR FYNHQVRVSA ADFVPSYHNQ QLPEWTELLQ SLSKAGYFSD SGSISGLESE
FFPGFPDELL RPALACLALA RERPELLEML SRRDVEVLVE NGKPFLFKTG PDSLKRMSLY
LRSGLQGIGK LMDMEKASTV DLMRLILSYV VDVASSEESK QHNKEIMESS VRSLLSQIAK
MSLRPPESNV HDTMQNQYSD RDGQGVRSFQ NNVEMKRGDW ICSRCSGMNF ARNVKCFQCD
EARPKRQLTG SEWECPQCDF YNYGRNVACL RCDCKRPRDS SLNSANSDYS SDPELERRLV
ENEKKAQRWL SKVAQGGSDA NSVDTDEDFP EIMPLRKGVN RYVVSTRKPP LERRLANTEN
RVATDGNSKR SDDNALGSKT TRSLNEILGS SSSLTSRSDD KNVSSRRFES SQGINTDFVP
FVPLPSDMFA KKPKEETQIG LIDNIQVDGF SGGNQNVYQE DKSDANHSGK ETDRLEKEDH
KSEEPARWFK RVTELHNVSD LESAIPQEIS PEKMPMRKGE NRFVVSRKKD RSLTSPAYKR
PEDSDFVPFV PFPPDYFAKE KQPKESIDTL PAPATENVSQ VVQQEPREPS INKSDTVAVK
IRNGKSLEGS LVKESDLLDM SEEAKAERWF KRVAEIKNIS ELSEIPDEDF PSIMPMRKGV
NRFVVSKRKT PLERRLTSQR HQRNPHITNS DPTGKGDK
