RAF1_SYNE7
ID RAF1_SYNE7 Reviewed; 356 AA.
AC Q31Q05;
DT 02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 60.
DE RecName: Full=RuBisCO accumulation factor 1 {ECO:0000255|HAMAP-Rule:MF_00856, ECO:0000303|PubMed:26237510};
GN Name=raf1 {ECO:0000255|HAMAP-Rule:MF_00856, ECO:0000303|PubMed:26237510};
GN OrderedLocusNames=Synpcc7942_0833;
OS Synechococcus elongatus (strain PCC 7942 / FACHB-805) (Anacystis nidulans
OS R2).
OC Bacteria; Cyanobacteria; Synechococcales; Synechococcaceae; Synechococcus.
OX NCBI_TaxID=1140;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 7942 / FACHB-805;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Schmutz J., Larimer F., Land M.,
RA Kyrpides N., Lykidis A., Richardson P.;
RT "Complete sequence of chromosome 1 of Synechococcus elongatus PCC 7942.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, INTERACTION WITH RBCL, SUBUNIT, DOMAIN, AND MUTAGENESIS OF
RP 60-ASN--GLN-67; SER-71; 94-TYR-GLU-95; 97-ARG-GLU-98; ARG-104;
RP 126-LYS--LYS-129; LYS-126; LYS-129; ARG-155; GLU-159; ARG-208;
RP 338-ARG--ARG-341 AND ARG-338.
RC STRAIN=PCC 7942 / FACHB-805;
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).
RN [3] {ECO:0007744|PDB:6SMH}
RP STRUCTURE BY ELECTRON MICROSCOPY (4.30 ANGSTROMS) OF 13-200 IN COMPLEX WITH
RP RUBISCO LARGE SUBUNIT (RBCL), FUNCTION, CARBOXYSOME ASSEMBLY PROCESS,
RP DOMAIN, AND DISRUPTION PHENOTYPE.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=32636267; DOI=10.1073/pnas.2007990117;
RA Huang F., Kong W.W., Sun Y., Chen T., Dykes G.F., Jiang Y.L., Liu L.N.;
RT "Rubisco accumulation factor 1 (Raf1) plays essential roles in mediating
RT Rubisco assembly and carboxysome biogenesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 117:17418-17428(2020).
CC -!- FUNCTION: A major RuBisCO chaperone. Acts after GroEL-GroES chaperonin
CC to fold and/or assemble the large subunit of RuBisCO (ccbL, rbcL).
CC Cooperates with RbcX in RbcL folding, plays the major role in assembly
CC of dimers into RbcL(8)-Raf1(8) intermediate complexes. RbcS replaces
CC Raf1, leading to holoenzyme formation. {ECO:0000255|HAMAP-
CC Rule:MF_00856}.
CC -!- FUNCTION: The Raf1 dimer brackets an RbcL dimer, leading to RbcL(8)-
CC Raf1(8) complex formation. RbcS displaces Raf1, resulting in holoenzyme
CC formation (PubMed:26237510, PubMed:32636267). Probably plays a role in
CC early carboxysome assembly; in its absence CcaA, CcmM, CcmN, RbcL and
CC RbcS colocalize in small patches while the shell proteins CcmK2, CcmK3
CC and CcmK4 are found diffused in the cytoplasm (PubMed:32636267).
CC {ECO:0000269|PubMed:26237510, ECO:0000269|PubMed:32636267}.
CC -!- FUNCTION: It has been suggested that Raf1 and RbcX are partially
CC functionally redundant (Probable). Other evidence suggests they are
CC antagonistic in mediating RuBisCO assembly (PubMed:32636267).
CC {ECO:0000269|PubMed:32636267, ECO:0000305|PubMed:26237510}.
CC -!- SUBUNIT: Homodimer. Forms an RbcL(8)-Raf1(8) complex. Forms complexes
CC of many stoichiometries with RbcL with and without RbcS. RbcX and Raf1
CC can bind simultaneously to RbcL. {ECO:0000255|HAMAP-Rule:MF_00856,
CC ECO:0000269|PubMed:26237510}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00856}.
CC -!- DOMAIN: Has 3 domains, the N-terminal alpha-helical domain, an extended
CC flexible linker and the C-terminal beta-sheet domain. The 2 C-terminal
CC beta-sheet domains are swapped and pack against each other to form the
CC dimer interface (By similarity). The N-terminal alpha-helical domain
CC stabilizes RbcL dimers and dimer-dimer interactions, facilitating
CC RbcL(8) formation. It binds to the same region of RbcL as RbcS
CC (PubMed:32636267). The C-terminal beta-sheet domain dimerizes Raf1
CC (Probable) (PubMed:32636267). {ECO:0000255|HAMAP-Rule:MF_00856,
CC ECO:0000269|PubMed:32636267, ECO:0000305|PubMed:32636267}.
CC -!- DISRUPTION PHENOTYPE: Decreased growth in ambient air, wild-type growth
CC on 3% CO(2). In ambient air about 30% decreased levels of RuBisCO,
CC decreased CO(2) fixation by whole cells. Carboxysome formation is
CC impaired; many small, irregular electron-dense structures are present
CC instead of the 3-4 large carboxysomes usually found in this strain, the
CC ratio of CcmM58:CcmM35 (involved in condensing RuBisCO) rises over 3-
CC fold. A double raf1-rbcX deletion partially recovers carboxysome
CC formation. {ECO:0000269|PubMed:32636267}.
CC -!- SIMILARITY: Belongs to the RAF family. {ECO:0000255|HAMAP-
CC Rule:MF_00856}.
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DR EMBL; CP000100; ABB56864.1; -; Genomic_DNA.
DR RefSeq; WP_011377752.1; NC_007604.1.
DR PDB; 6SMH; EM; 4.30 A; I/J/K/L/M/N/O/P=13-200.
DR PDBsum; 6SMH; -.
DR AlphaFoldDB; Q31Q05; -.
DR SMR; Q31Q05; -.
DR STRING; 1140.Synpcc7942_0833; -.
DR PRIDE; Q31Q05; -.
DR EnsemblBacteria; ABB56864; ABB56864; Synpcc7942_0833.
DR KEGG; syf:Synpcc7942_0833; -.
DR eggNOG; ENOG502Z7IG; Bacteria.
DR HOGENOM; CLU_766477_0_0_3; -.
DR OMA; IVASQVY; -.
DR OrthoDB; 951992at2; -.
DR BioCyc; SYNEL:SYNPCC7942_0833-MON; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0015977; P:carbon fixation; IEA:UniProtKB-KW.
DR GO; GO:0015979; P:photosynthesis; IEA:UniProtKB-KW.
DR GO; GO:0110102; P:ribulose bisphosphate carboxylase complex assembly; IDA:UniProtKB.
DR HAMAP; MF_00856; Raf1; 1.
DR InterPro; IPR037494; RAF1.
DR InterPro; IPR040858; Raf1_C.
DR InterPro; IPR046382; Raf1_cyn.
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; Carbon dioxide fixation; Chaperone; Cytoplasm;
KW Photosynthesis.
FT CHAIN 1..356
FT /note="RuBisCO accumulation factor 1"
FT /id="PRO_0000451577"
FT REGION 9..192
FT /note="N-terminal alpha-helix"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00856,
FT ECO:0000305|PubMed:26237510"
FT REGION 216..342
FT /note="C-terminal beta-sheet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00856,
FT ECO:0000305|PubMed:26237510"
FT MUTAGEN 60..67
FT /note="NQITVAMQ->AQITAAMA: Increases RbcL(8)-Raf1 complex
FT formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 71
FT /note="S->A: Increases RbcL(8)-Raf1 complex formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 94..95
FT /note="YE->AA: Increases RbcL(8)-Raf1 complex formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 97..98
FT /note="RE->AA: Increases RbcL(8)-Raf1 complex formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 104
FT /note="R->Q: Increases RbcL(8)-Raf1 complex formation,
FT decreases RuBisCO holoenzyme formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 126..129
FT /note="KATK->AATA: Increases RbcL(8)-Raf1 complex
FT formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 126
FT /note="K->A: Increases RbcL(8)-Raf1 complex formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 129
FT /note="K->A: Increases RbcL(8)-Raf1 complex formation,
FT decreases RuBisCO holoenzyme formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 155
FT /note="R->A: Increases RbcL(8)-Raf1 complex formation."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 159
FT /note="E->A: Wild type."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 208
FT /note="R->A: Incomplete conversion of RbcL(2)-Raf1 to
FT holoenzyme."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 338..341
FT /note="RPKR->APKA: Incomplete conversion of RbcL(2)-Raf1 to
FT holoenzyme."
FT /evidence="ECO:0000269|PubMed:26237510"
FT MUTAGEN 338
FT /note="R->A: Incomplete conversion of RbcL(2)-Raf1 to
FT holoenzyme."
FT /evidence="ECO:0000269|PubMed:26237510"
SQ SEQUENCE 356 AA; 40160 MW; 06709F2862DD6361 CRC64;
MREFTPTTLS EEERQELLGQ LRRKEGRWLA WARACQTLLK NGLNPQTLFE ATGFEPIQQN
QITVAMQVYD SILRQDPPAH VRETYQEWGS DLLYELRELD QEQRSLCAQL ALERKLDADQ
IREVAKATKD FCRLPKQPEN FDRHPGDAVA HQCWRLAQER TDLTERSRLI ARGLQFAQSA
GARALIEALL LDLSGVPSRK PPMLPIYRLE TEEDLPRLLP FAGTLPLSSS QIEAIAAVEA
EGPFGLVSSP QGQQWLALPG WQAILTAEDP IACLEQIDRL PNAPEGPTEA VVLVVDRADR
DWDADHFFLV EQAEGARIQW SPSAIAAPIL GRLVLILRPK RVLDEAAIAT PWQFEE
