RAF1_ARATH
ID RAF1_ARATH Reviewed; 434 AA.
AC Q9LKR8; F4K8I9;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Rubisco accumulation factor 1.1, chloroplastic {ECO:0000303|PubMed:22942379};
DE Flags: Precursor;
GN Name=RAF1.1 {ECO:0000303|PubMed:22942379};
GN OrderedLocusNames=At5g28500 {ECO:0000312|Araport:AT5G28500};
GN ORFNames=T26D3.4 {ECO:0000312|EMBL:AAF88015.1};
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] (ISOFORM 1).
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Shinn P., Chen H., Cheuk R., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP IDENTIFICATION.
RX PubMed=22942379; DOI=10.1105/tpc.112.102012;
RA Feiz L., Williams-Carrier R., Wostrikoff K., Belcher S., Barkan A.,
RA Stern D.B.;
RT "Ribulose-1,5-bis-phosphate carboxylase/oxygenase accumulation factor1 is
RT required for holoenzyme assembly in maize.";
RL Plant Cell 24:3435-3446(2012).
RN [6]
RP SUBUNIT.
RX PubMed=26237510; DOI=10.1038/nsmb.3062;
RA Hauser T., Bhat J.Y., Milicic G., Wendler P., Hartl F.U., Bracher A.,
RA Hayer-Hartl M.;
RT "Structure and mechanism of the Rubisco-assembly chaperone Raf1.";
RL Nat. Struct. Mol. Biol. 22:720-728(2015).
CC -!- FUNCTION: Required for assembly or stability of RuBisCO. Acts at a
CC postchaperonin step to fold and/or assemble the large subunit (rbcL)
CC into RuBisCO. RAF1 binds first to a rbcL dimer (rbcL(2)), leading to a
CC rbcL(8)-RAF1(4) complex formation. In the next step, RBCS displaces
CC RAF1, thus resulting in holoenzyme formation.
CC {ECO:0000250|UniProtKB:Q9SR19}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:26237510}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LKR8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LKR8-2; Sequence=VSP_053355, VSP_053356;
CC -!- DOMAIN: Has 3 domains, the N-terminal alpha-helical domain, an extended
CC flexible linker and the C-terminal beta-sheet domain. The N-terminal
CC alpha-helical domain stabilizes RbcL dimers and RbcL dimer-dimer
CC interactions, facilitating RbcL(8) formation. The C-terminal beta-sheet
CC domain probably dimerizes Raf1 (PubMed:26237510). The 2 C-terminal
CC beta-sheet domains are swapped and pack against each other to form the
CC dimer interface (By similarity). {ECO:0000250|UniProtKB:Q8YLP6,
CC ECO:0000269|PubMed:26237510}.
CC -!- SIMILARITY: Belongs to the RAF family. {ECO:0000305}.
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DR EMBL; AF262043; AAF88015.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93807.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93808.1; -; Genomic_DNA.
DR EMBL; BT000776; AAN31915.1; -; mRNA.
DR EMBL; BT015787; AAU90077.1; -; mRNA.
DR RefSeq; NP_001190416.1; NM_001203487.1. [Q9LKR8-2]
DR RefSeq; NP_198202.1; NM_122733.3. [Q9LKR8-1]
DR AlphaFoldDB; Q9LKR8; -.
DR SMR; Q9LKR8; -.
DR BioGRID; 18216; 1.
DR STRING; 3702.AT5G28500.1; -.
DR iPTMnet; Q9LKR8; -.
DR PaxDb; Q9LKR8; -.
DR PRIDE; Q9LKR8; -.
DR ProMEX; Q9LKR8; -.
DR ProteomicsDB; 236503; -. [Q9LKR8-1]
DR EnsemblPlants; AT5G28500.1; AT5G28500.1; AT5G28500. [Q9LKR8-1]
DR EnsemblPlants; AT5G28500.2; AT5G28500.2; AT5G28500. [Q9LKR8-2]
DR GeneID; 832943; -.
DR Gramene; AT5G28500.1; AT5G28500.1; AT5G28500. [Q9LKR8-1]
DR Gramene; AT5G28500.2; AT5G28500.2; AT5G28500. [Q9LKR8-2]
DR KEGG; ath:AT5G28500; -.
DR Araport; AT5G28500; -.
DR TAIR; locus:2182763; AT5G28500.
DR eggNOG; ENOG502QRYH; Eukaryota.
DR HOGENOM; CLU_041979_0_0_1; -.
DR InParanoid; Q9LKR8; -.
DR OMA; IVASQVY; -.
DR OrthoDB; 1337198at2759; -.
DR PhylomeDB; Q9LKR8; -.
DR PRO; PR:Q9LKR8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LKR8; baseline and differential.
DR Genevisible; Q9LKR8; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0110102; P:ribulose bisphosphate carboxylase complex assembly; IEA:UniProt.
DR InterPro; IPR037494; RAF1.
DR InterPro; IPR040858; Raf1_C.
DR InterPro; IPR040781; Raf1_HTH.
DR InterPro; IPR041358; Raf1_N.
DR PANTHER; PTHR35299; PTHR35299; 1.
DR Pfam; PF18579; Raf1_HTH; 1.
DR Pfam; PF18578; Raf1_N; 1.
DR Pfam; PF18087; RuBisCo_chap_C; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chaperone; Chloroplast; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..51
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 52..434
FT /note="Rubisco accumulation factor 1.1, chloroplastic"
FT /id="PRO_0000424242"
FT REGION 65..254
FT /note="N-terminal alpha-helix"
FT /evidence="ECO:0000305|PubMed:26237510"
FT REGION 273..419
FT /note="C-terminal beta sheet"
FT /evidence="ECO:0000305|PubMed:26237510"
FT VAR_SEQ 263..269
FT /note="VKEEEIK -> GKEDGGS (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_053355"
FT VAR_SEQ 270..434
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_053356"
SQ SEQUENCE 434 AA; 48237 MW; 40045E6E8BD38D2A CRC64;
MLSLTATTLS SSIFTQSKTH GFFNTRPVYR KPFTTITSAL IPASNRQAPP KQQLYQPFRP
PPSPIPPKFR SLDTAGKIEV LADRLGLWFE YAPLISSLYT EGFTPPSIEE LTGISGVEQN
SLIVGAQVRD SLVQSGAKPE LIAAFDTNGA ELLYEIRLLN TTQRVAAAEY IVDHGFDTKG
AGDLARAIKD FPHRRGDVGL GDFDYNLPGD CLSFMLYRKS REHRSPSEIR TTLLEQALET
AVTEKAKKAV LRELHGESEE ERVKEEEIKI IRVPVVRLRF GEVAGASSVV VLPVCKAEEG
EEKLLEAPME FESGGEFGVV EAEKDWSRWV VLPGWDPVVA VRKGVAVSFS DDREVLPWNG
KGEAIMVVID REKKTVEADN GYYYLVVADG GMKLDRGLVL KEKGVNESLG MVVLVVRPPR
DDDDEWQIND EDWD
