RAF2_ARATH
ID RAF2_ARATH Reviewed; 449 AA.
AC Q9SR19;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 113.
DE RecName: Full=Rubisco accumulation factor 1.2, chloroplastic {ECO:0000303|PubMed:22942379};
DE Flags: Precursor;
GN Name=RAF1.2 {ECO:0000303|PubMed:22942379};
GN OrderedLocusNames=At3g04550 {ECO:0000312|Araport:AT3G04550};
GN ORFNames=F7O18.2 {ECO:0000312|EMBL:AAF04886.1};
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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].
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 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 [5] {ECO:0007744|PDB:4WT3, ECO:0007744|PDB:4WT4, ECO:0007744|PDB:4WT5}
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 62-274, X-RAY CRYSTALLOGRAPHY
RP (2.57 ANGSTROMS) OF 281-449, SUBUNIT, AND FUNCTION.
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 brackets an rbcL dimer (rbcL(2)), leading to
CC rbcL(8)-RAF1(4) complex formation. In the next step, RBCS displaces
CC RAF1, thus resulting in holoenzyme formation.
CC {ECO:0000269|PubMed:26237510}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:26237510}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
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 (PubMed:26237510). The C-
CC terminal beta-sheet domain probably dimerizes Raf1 (Probable). The 2 C-
CC terminal beta-sheet domains are swapped and pack against each other to
CC form the dimer interface (By similarity).
CC {ECO:0000250|UniProtKB:Q8YLP6, ECO:0000269|PubMed:26237510,
CC ECO:0000305|PubMed:26237510}.
CC -!- SIMILARITY: Belongs to the RAF family. {ECO:0000305}.
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DR EMBL; AC011437; AAF04886.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74096.1; -; Genomic_DNA.
DR EMBL; AY034914; AAK59421.1; -; mRNA.
DR EMBL; AY062440; AAL32518.1; -; mRNA.
DR EMBL; AY063107; AAL34281.1; -; mRNA.
DR EMBL; AY114629; AAM47948.1; -; mRNA.
DR RefSeq; NP_566230.1; NM_111326.1.
DR PDB; 4WT3; X-ray; 1.95 A; A=62-274.
DR PDB; 4WT4; X-ray; 2.81 A; A/B/C/D=281-449.
DR PDB; 4WT5; X-ray; 2.57 A; A/B=281-449.
DR PDBsum; 4WT3; -.
DR PDBsum; 4WT4; -.
DR PDBsum; 4WT5; -.
DR AlphaFoldDB; Q9SR19; -.
DR SMR; Q9SR19; -.
DR STRING; 3702.AT3G04550.1; -.
DR MetOSite; Q9SR19; -.
DR PaxDb; Q9SR19; -.
DR PRIDE; Q9SR19; -.
DR ProMEX; Q9SR19; -.
DR ProteomicsDB; 225966; -.
DR EnsemblPlants; AT3G04550.1; AT3G04550.1; AT3G04550.
DR GeneID; 819611; -.
DR Gramene; AT3G04550.1; AT3G04550.1; AT3G04550.
DR KEGG; ath:AT3G04550; -.
DR Araport; AT3G04550; -.
DR TAIR; locus:2084888; AT3G04550.
DR eggNOG; ENOG502QRYH; Eukaryota.
DR HOGENOM; CLU_041979_0_0_1; -.
DR InParanoid; Q9SR19; -.
DR OMA; VGWLDFD; -.
DR OrthoDB; 1337198at2759; -.
DR PhylomeDB; Q9SR19; -.
DR PRO; PR:Q9SR19; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SR19; baseline and differential.
DR Genevisible; Q9SR19; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0110102; P:ribulose bisphosphate carboxylase complex assembly; IDA:TAIR.
DR DisProt; DP02961; -.
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 3D-structure; Chaperone; Chloroplast; Coiled coil; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..61
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 62..449
FT /note="Rubisco accumulation factor 1.2, chloroplastic"
FT /id="PRO_0000424243"
FT REGION 75..264
FT /note="N-terminal alpha-helix"
FT /evidence="ECO:0000305|PubMed:26237510"
FT REGION 288..434
FT /note="C-terminal beta sheet"
FT /evidence="ECO:0000305|PubMed:26237510"
FT COILED 262..288
FT /evidence="ECO:0000255"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 84..92
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 98..111
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 115..122
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 126..144
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 149..153
FT /evidence="ECO:0007829|PDB:4WT3"
FT TURN 154..158
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 160..165
FT /evidence="ECO:0007829|PDB:4WT3"
FT TURN 166..168
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 171..183
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 188..200
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 201..204
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 218..232
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 238..250
FT /evidence="ECO:0007829|PDB:4WT3"
FT HELIX 254..265
FT /evidence="ECO:0007829|PDB:4WT3"
FT STRAND 290..292
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 302..311
FT /evidence="ECO:0007829|PDB:4WT5"
FT HELIX 312..314
FT /evidence="ECO:0007829|PDB:4WT5"
FT HELIX 316..321
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 326..329
FT /evidence="ECO:0007829|PDB:4WT5"
FT TURN 330..333
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 334..339
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 342..348
FT /evidence="ECO:0007829|PDB:4WT5"
FT HELIX 351..355
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 360..365
FT /evidence="ECO:0007829|PDB:4WT5"
FT TURN 369..371
FT /evidence="ECO:0007829|PDB:4WT4"
FT STRAND 381..387
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 398..403
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 406..411
FT /evidence="ECO:0007829|PDB:4WT5"
FT HELIX 412..417
FT /evidence="ECO:0007829|PDB:4WT5"
FT STRAND 424..432
FT /evidence="ECO:0007829|PDB:4WT5"
SQ SEQUENCE 449 AA; 50199 MW; 93AC5639705D11CC CRC64;
MFSLKSLISS PFTQSTTHGL FTNPITRPVN PLPRTVSFTV TASMIPKRSS ANMIPKNPPA
RQQLYQPFRP PSSPIPTQFR SLDSAGKIEI LAGRMALWFE YAPLISSLYT DGFTPPTIEE
LTGISSIEQN RLIVGAQVRD SILQSIHEPE LISAFDTGGA ELLYEIRLLS TTQRVAAATF
IIDRNIDSKG AQDLARAIKD YPNRRGDVGW LDFDYNLPGD CLSFLYYRQS RENKNPSDQR
TSMLLQALGV AESEKAKNRL NTELYGDKEA EKEKEKKKKE EEVKAIRIPV VRLKFGEVAE
ATSVVVLPVC KAEEGEKKIL EAPMEIIAGG DFKVVEAEKG WKRWVVLPSW NPVAAIGKGG
VAVSFRDDRK VLPWDGKEEP LLVVADRVRN VVEADDGYYL VVAENGLKLE KGSDLKAREV
KESLGMVVLV VRPPREDDDD WQTSHQNWD
