CCMK4_SYNE7
ID CCMK4_SYNE7 Reviewed; 113 AA.
AC Q31RK2;
DT 07-OCT-2020, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=Carboxysome shell protein CcmK4 {ECO:0000303|PubMed:22928045};
DE AltName: Full=Carbon dioxide-concentrating mechanism protein CcmK4;
GN Name=ccmK4 {ECO:0000303|PubMed:22928045};
GN OrderedLocusNames=Synpcc7942_0285;
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, AND DISRUPTION PHENOTYPE.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=22928045; DOI=10.1371/journal.pone.0043871;
RA Rae B.D., Long B.M., Badger M.R., Price G.D.;
RT "Structural determinants of the outer shell of beta-carboxysomes in
RT Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL.";
RL PLoS ONE 7:e43871-e43871(2012).
RN [3]
RP SUBCELLULAR LOCATION.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=28963440; DOI=10.1091/mbc.e17-01-0069;
RA Niederhuber M.J., Lambert T.J., Yapp C., Silver P.A., Polka J.K.;
RT "Superresolution microscopy of the beta-carboxysome reveals a homogeneous
RT matrix.";
RL Mol. Biol. Cell 28:2734-2745(2017).
RN [4]
RP SUBCELLULAR LOCATION.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=28616951; DOI=10.1039/c7nr02524f;
RA Faulkner M., Rodriguez-Ramos J., Dykes G.F., Owen S.V., Casella S.,
RA Simpson D.M., Beynon R.J., Liu L.N.;
RT "Direct characterization of the native structure and mechanics of
RT cyanobacterial carboxysomes.";
RL Nanoscale 9:10662-10673(2017).
RN [5]
RP BIOTECHNOLOGY.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=29922315; DOI=10.3389/fpls.2018.00739;
RA Fang Y., Huang F., Faulkner M., Jiang Q., Dykes G.F., Yang M., Liu L.N.;
RT "Engineering and Modulating Functional Cyanobacterial CO2-Fixing
RT Organelles.";
RL Front. Plant Sci. 9:739-739(2018).
RN [6]
RP SUBCELLULAR LOCATION, AND INDUCTION.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=31048338; DOI=10.1105/tpc.18.00787;
RA Sun Y., Wollman A.J.M., Huang F., Leake M.C., Liu L.N.;
RT "Single-Organelle Quantification Reveals Stoichiometric and Structural
RT Variability of Carboxysomes Dependent on the Environment.";
RL Plant Cell 31:1648-1664(2019).
RN [7]
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF SER-40.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=30389783; DOI=10.1104/pp.18.01190;
RA Sommer M., Sutter M., Gupta S., Kirst H., Turmo A., Lechno-Yossef S.,
RA Burton R.L., Saechao C., Sloan N.B., Cheng X., Chan L.G., Petzold C.J.,
RA Fuentes-Cabrera M., Ralston C.Y., Kerfeld C.A.;
RT "Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta
RT Carboxysome Shells.";
RL Plant Physiol. 179:156-167(2019).
RN [8]
RP SUBUNIT.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=31603944; DOI=10.1371/journal.pone.0223877;
RA Garcia-Alles L.F., Root K., Maveyraud L., Aubry N., Lesniewska E.,
RA Mourey L., Zenobi R., Truan G.;
RT "Occurrence and stability of hetero-hexamer associations formed by beta-
RT carboxysome CcmK shell components.";
RL PLoS ONE 14:e0223877-e0223877(2019).
RN [9] {ECO:0007744|PDB:4OX6}
RP X-RAY CRYSTALLOGRAPHY (1.34 ANGSTROMS), SUBUNIT, SUBCELLULAR LOCATION,
RP DOMAIN, AND MUTAGENESIS OF 36-MET--ALA-38.
RC STRAIN=PCC 7942 / FACHB-805;
RX PubMed=25117559; DOI=10.1021/sb500226j;
RA Cai F., Sutter M., Bernstein S.L., Kinney J.N., Kerfeld C.A.;
RT "Engineering bacterial microcompartment shells: chimeric shell proteins and
RT chimeric carboxysome shells.";
RL ACS Synth. Biol. 4:444-453(2015).
CC -!- FUNCTION: One of the shell proteins of the carboxysome, a polyhedral
CC inclusion where RuBisCO (ribulose bisphosphate carboxylase, rbcL-rbcS)
CC is sequestered. Assembles into hexamers which make sheets that form the
CC facets of the polyhedral carboxysome. The hexamer central pore probably
CC regulates metabolite flux. {ECO:0000255|HAMAP-Rule:MF_00854}.
CC -!- FUNCTION: A minor shell protein of the carboxysome, a polyhedral
CC inclusion where RuBisCO (ribulose bisphosphate carboxylase, rbcL-rbcS)
CC is sequestered (Probable). Hexamers form sheets that form the facets of
CC the polyhedral carboxysome. The shell is 4.5 nm thick, as observed for
CC CcmK proteins (PubMed:28616951). In PCC 7942 there are several CcmK
CC paralogs with presumably functional differences; replacing the central
CC pore residues (34-37) with those of CcmK2 from this organism (Tyr-Glu-
CC Lys-Ile) allows the bacterium to make carboxysomes, but the expression
CC level is too low to know if the carboxysome is functional for CO(2)
CC fixation (Probable). This subunit probably makes both homohexamers and
CC heterohexamers with CcmK3. The CcmK3-CcmK4 heterohexmers have been
CC suggested to cap other hexamers, perhaps to alter metabolite flux
CC (Probable). {ECO:0000269|PubMed:28616951, ECO:0000305|PubMed:22928045,
CC ECO:0000305|PubMed:25117559, ECO:0000305|PubMed:30389783}.
CC -!- SUBUNIT: Homohexamer (PubMed:25117559). Interacts stably with CcmK3,
CC probably forms heterohexamers with a 1:2 CcmK3:CcmK4 stoichiometry
CC (PubMed:30389783) (Probable). {ECO:0000269|PubMed:25117559,
CC ECO:0000269|PubMed:30389783, ECO:0000305|PubMed:31603944}.
CC -!- SUBCELLULAR LOCATION: Carboxysome {ECO:0000255|HAMAP-Rule:MF_00854,
CC ECO:0000269|PubMed:25117559, ECO:0000269|PubMed:28616951,
CC ECO:0000269|PubMed:28963440, ECO:0000269|PubMed:31048338}. Note=This
CC cyanobacterium makes beta-type carboxysomes (PubMed:25117559). Part of
CC the carboxysome shell, not found in the interior (PubMed:28963440).
CC {ECO:0000269|PubMed:25117559, ECO:0000269|PubMed:28963440}.
CC -!- INDUCTION: Carboxysome size and components vary with growth conditions.
CC When grown in ambient air at medium light (50 uE meter(-2) second(-1))
CC there are 52 units of this protein per carboxysome, the numbers are
CC stable under low light and high light, and increase under high CO(2)
CC (at protein level). The CcmK3:CcmK4 ratio of 1:3.8 is stable over all
CC growth conditions. {ECO:0000269|PubMed:31048338}.
CC -!- DOMAIN: The tight homohexamer forms a pore with an opening of about 5
CC Angstroms in diameter and is positively charged.
CC {ECO:0000269|PubMed:25117559}.
CC -!- DISRUPTION PHENOTYPE: Single deletion has a wild-type phenotype, a
CC double ccmK3-ccmK4 deletion has slightly larger, aggregated instead of
CC spatially separated carboxysomes, and has a photosynthetic affinity for
CC inorganic carbon between wild-type and carboxysome-less strains
CC (PubMed:22928045). In another study single mutant grows slower in air
CC and low light, double ccmK3-ccmK4 mutant has similarly impaired growth
CC rate; ccmK3 does not complement the double deletion, while ccmK4 does
CC (PubMed:30389783). {ECO:0000269|PubMed:22928045,
CC ECO:0000269|PubMed:30389783}.
CC -!- BIOTECHNOLOGY: Heterologous expression of 12 carboxysomal genes in
CC E.coli (ccaA, ccmK2, ccmK3, ccmK4, ccmL, ccmM, ccmN, ccmO, ccmP, rbcL,
CC rbcS, rbcX) leads to the formation of bodies that resemble
CC carboxysomes, have densely packed paracrystalline arrays and RuBisCO
CC activity. These structures open the door to generating carboxysomes in
CC plant cells to increase their photosynthesis and productivity, as well
CC as tailoring bacterial microcompartments to specific metabolic needs
CC and molecule delivery. The absence of ccaA, ccmK3, ccmK4, ccmP and rbcX
CC leads to less active RuBisCO. {ECO:0000269|PubMed:29922315}.
CC -!- SIMILARITY: Belongs to the bacterial microcompartments protein family.
CC CcmK subfamily. {ECO:0000255|HAMAP-Rule:MF_00854}.
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DR EMBL; CP000100; ABB56317.1; -; Genomic_DNA.
DR RefSeq; WP_011243539.1; NC_007604.1.
DR PDB; 4OX6; X-ray; 1.34 A; A/B=1-113.
DR PDBsum; 4OX6; -.
DR AlphaFoldDB; Q31RK2; -.
DR SMR; Q31RK2; -.
DR STRING; 1140.Synpcc7942_0285; -.
DR PRIDE; Q31RK2; -.
DR EnsemblBacteria; ABB56317; ABB56317; Synpcc7942_0285.
DR KEGG; syf:Synpcc7942_0285; -.
DR eggNOG; COG4577; Bacteria.
DR HOGENOM; CLU_064903_5_0_3; -.
DR OMA; ESWVIIP; -.
DR OrthoDB; 1802372at2; -.
DR BioCyc; SYNEL:SYNPCC7942_0285-MON; -.
DR GO; GO:0031470; C:carboxysome; IDA:UniProtKB.
DR GO; GO:0043886; F:structural constituent of carboxysome; IMP:UniProtKB.
DR GO; GO:0015977; P:carbon fixation; IEA:UniProtKB-KW.
DR GO; GO:0015979; P:photosynthesis; IEA:UniProtKB-KW.
DR Gene3D; 3.30.70.1710; -; 1.
DR HAMAP; MF_00854; CcmK; 1.
DR InterPro; IPR020808; Bact_microcomp_CS.
DR InterPro; IPR000249; BMC_dom.
DR InterPro; IPR046380; CcmK.
DR InterPro; IPR037233; CcmK-like_sf.
DR InterPro; IPR044872; CcmK/CsoS1_BMC.
DR Pfam; PF00936; BMC; 1.
DR SMART; SM00877; BMC; 1.
DR SUPFAM; SSF143414; SSF143414; 1.
DR PROSITE; PS01139; BMC_1; 1.
DR PROSITE; PS51930; BMC_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial microcompartment; Carbon dioxide fixation;
KW Carboxysome; Photosynthesis.
FT CHAIN 1..113
FT /note="Carboxysome shell protein CcmK4"
FT /id="PRO_0000451236"
FT DOMAIN 5..91
FT /note="BMC"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00854"
FT MUTAGEN 36..38
FT /note="MRA->EKI: Probably alters pore properties, is able
FT to form carboxysomes, residues correspond to CcmK2 of this
FT organism."
FT /evidence="ECO:0000269|PubMed:25117559"
FT MUTAGEN 40
FT /note="S->D: Does not complement its deletion mutant, forms
FT homohexamers in vitro."
FT /evidence="ECO:0000269|PubMed:30389783"
FT STRAND 3..13
FT /evidence="ECO:0007829|PDB:4OX6"
FT HELIX 14..25
FT /evidence="ECO:0007829|PDB:4OX6"
FT STRAND 31..39
FT /evidence="ECO:0007829|PDB:4OX6"
FT STRAND 42..49
FT /evidence="ECO:0007829|PDB:4OX6"
FT HELIX 51..67
FT /evidence="ECO:0007829|PDB:4OX6"
FT STRAND 72..81
FT /evidence="ECO:0007829|PDB:4OX6"
FT HELIX 84..89
FT /evidence="ECO:0007829|PDB:4OX6"
FT HELIX 96..101
FT /evidence="ECO:0007829|PDB:4OX6"
SQ SEQUENCE 113 AA; 11946 MW; A961559E472C2545 CRC64;
MSQQAIGSLE TKGFPPILAA ADAMVKAGRI TIVSYMRAGS ARFAVNIRGD VSEVKTAMDA
GIEAAKNTPG GTLETWVIIP RPHENVEAVF PIGFGPEVEQ YRLSAEGTGS GRR
