RBL1B_HYDCU
ID RBL1B_HYDCU Reviewed; 471 AA.
AC Q31HD9;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Ribulose bisphosphate carboxylase large chain 2 {ECO:0000255|HAMAP-Rule:MF_01338};
DE Short=RuBisCO large subunit 2 {ECO:0000255|HAMAP-Rule:MF_01338};
DE EC=4.1.1.39 {ECO:0000255|HAMAP-Rule:MF_01338, ECO:0000269|PubMed:18974784, ECO:0000269|PubMed:26581415};
DE AltName: Full=Carboxysomal form I RuBisCO large subunit {ECO:0000303|PubMed:28115547};
GN Name=cbbL2 {ECO:0000255|HAMAP-Rule:MF_01338}; OrderedLocusNames=Tcr_0838;
OS Hydrogenovibrio crunogenus (strain DSM 25203 / XCL-2) (Thiomicrospira
OS crunogena).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales;
OC Piscirickettsiaceae; Hydrogenovibrio.
OX NCBI_TaxID=317025;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 25203 / XCL-2;
RX PubMed=17105352; DOI=10.1371/journal.pbio.0040383;
RA Scott K.M., Sievert S.M., Abril F.N., Ball L.A., Barrett C.J., Blake R.A.,
RA Boller A.J., Chain P.S.G., Clark J.A., Davis C.R., Detter C., Do K.F.,
RA Dobrinski K.P., Faza B.I., Fitzpatrick K.A., Freyermuth S.K., Harmer T.L.,
RA Hauser L.J., Huegler M., Kerfeld C.A., Klotz M.G., Kong W.W., Land M.,
RA Lapidus A., Larimer F.W., Longo D.L., Lucas S., Malfatti S.A., Massey S.E.,
RA Martin D.D., McCuddin Z., Meyer F., Moore J.L., Ocampo L.H. Jr., Paul J.H.,
RA Paulsen I.T., Reep D.K., Ren Q., Ross R.L., Sato P.Y., Thomas P.,
RA Tinkham L.E., Zeruth G.T.;
RT "The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena
RT XCL-2.";
RL PLoS Biol. 4:1-17(2006).
RN [2]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=DSM 25203 / XCL-2;
RX PubMed=18974784; DOI=10.1371/journal.pone.0003570;
RA Menon B.B., Dou Z., Heinhorst S., Shively J.M., Cannon G.C.;
RT "Halothiobacillus neapolitanus carboxysomes sequester heterologous and
RT chimeric RubisCO species.";
RL PLoS ONE 3:e3570-e3570(2008).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=DSM 25203 / XCL-2;
RX PubMed=26581415; DOI=10.1007/s00203-015-1172-6;
RG USF MCB4404L 2012;
RA Menning K.J., Menon B.B., Fox G., Scott K.M.;
RT "Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is
RT Deltap- and ATP-sensitive and enhances RubisCO-mediated carbon fixation.";
RL Arch. Microbiol. 198:149-159(2016).
RN [4]
RP INDUCTION.
RC STRAIN=DSM 25203 / XCL-2;
RX PubMed=28115547; DOI=10.1128/jb.00871-16;
RG USF MCB4404L;
RA Mangiapia M., Brown T.W., Chaput D., Haller E., Harmer T.L., Hashemy Z.,
RA Keeley R., Leonard J., Mancera P., Nicholson D., Stevens S., Wanjugi P.,
RA Zabinski T., Pan C., Scott K.M.;
RT "Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of
RT Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena.";
RL J. Bacteriol. 199:0-0(2017).
CC -!- FUNCTION: RuBisCO catalyzes two reactions: the carboxylation of D-
CC ribulose 1,5-bisphosphate, the primary event in carbon dioxide
CC fixation, as well as the oxidative fragmentation of the pentose
CC substrate. Both reactions occur simultaneously and in competition at
CC the same active site (By similarity). Replacing the endogenous type I
CC ccbLS genes in H.neapolitanus with this carboxysomally targeted enzyme
CC reconstitutes RuBisCO with about 25% of normal activity; the active
CC enzyme is targeted to carboxysomes (PubMed:18974784).
CC {ECO:0000255|HAMAP-Rule:MF_01338, ECO:0000269|PubMed:18974784}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-
CC bisphosphate + H2O; Xref=Rhea:RHEA:23124, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57870,
CC ChEBI:CHEBI:58272; EC=4.1.1.39; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01338, ECO:0000269|PubMed:26581415};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate +
CC 2-phosphoglycolate + 2 H(+); Xref=Rhea:RHEA:36631, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:57870, ChEBI:CHEBI:58033,
CC ChEBI:CHEBI:58272; Evidence={ECO:0000255|HAMAP-Rule:MF_01338};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01338};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01338};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=276 uM for CO(2) {ECO:0000269|PubMed:26581415};
CC Vmax=252 nmol/min/mg enzyme {ECO:0000269|PubMed:26581415};
CC Note=kcat is 0.27 sec(-1) for holoenzyme.
CC {ECO:0000269|PubMed:26581415};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:26581415};
CC -!- SUBUNIT: Heterohexadecamer of 8 large chains and 8 small chains. Forms
CC a CsoS2-CsoS1-RuBisCO complex (By similarity).
CC {ECO:0000250|UniProtKB:O85040, ECO:0000255|HAMAP-Rule:MF_01338}.
CC -!- SUBCELLULAR LOCATION: Carboxysome {ECO:0000269|PubMed:26581415,
CC ECO:0000305|PubMed:17105352, ECO:0000305|PubMed:18974784}. Note=This
CC bacterium makes alpha-type carboxysomes. {ECO:0000305}.
CC -!- INDUCTION: Induced by growth in low levels of dissolved inorganic
CC carbon (at protein level). {ECO:0000269|PubMed:28115547}.
CC -!- MISCELLANEOUS: Encoded in a cso-type operon.
CC {ECO:0000269|PubMed:17105352}.
CC -!- MISCELLANEOUS: The basic functional RuBisCO is composed of a large
CC chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO
CC this homodimer is arranged in a barrel-like tetramer with the small
CC subunits forming a tetrameric 'cap' on each end of the 'barrel'.
CC {ECO:0000255|HAMAP-Rule:MF_01338}.
CC -!- SIMILARITY: Belongs to the RuBisCO large chain family. Type I
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01338}.
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DR EMBL; CP000109; ABB41434.1; -; Genomic_DNA.
DR RefSeq; WP_011370261.1; NC_007520.2.
DR AlphaFoldDB; Q31HD9; -.
DR SMR; Q31HD9; -.
DR STRING; 317025.Tcr_0838; -.
DR EnsemblBacteria; ABB41434; ABB41434; Tcr_0838.
DR KEGG; tcx:Tcr_0838; -.
DR eggNOG; COG1850; Bacteria.
DR HOGENOM; CLU_031450_2_0_6; -.
DR OMA; GGGTQGH; -.
DR OrthoDB; 848380at2; -.
DR GO; GO:0031470; C:carboxysome; IEA:UniProtKB-SubCell.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0016984; F:ribulose-bisphosphate carboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019253; P:reductive pentose-phosphate cycle; IEA:UniProtKB-UniRule.
DR Gene3D; 3.20.20.110; -; 1.
DR Gene3D; 3.30.70.150; -; 1.
DR HAMAP; MF_01338; RuBisCO_L_type1; 1.
DR InterPro; IPR033966; RuBisCO.
DR InterPro; IPR000685; RuBisCO_lsu_C.
DR InterPro; IPR036376; RuBisCO_lsu_C_sf.
DR InterPro; IPR017443; RuBisCO_lsu_fd_N.
DR InterPro; IPR036422; RuBisCO_lsu_N_sf.
DR InterPro; IPR020888; RuBisCO_lsuI.
DR PANTHER; PTHR42704; PTHR42704; 1.
DR Pfam; PF00016; RuBisCO_large; 1.
DR Pfam; PF02788; RuBisCO_large_N; 1.
DR SFLD; SFLDS00014; RuBisCO; 1.
DR SUPFAM; SSF51649; SSF51649; 1.
DR SUPFAM; SSF54966; SSF54966; 1.
PE 1: Evidence at protein level;
KW Bacterial microcompartment; Calvin cycle; Carbon dioxide fixation;
KW Carboxysome; Lyase; Magnesium; Metal-binding; Monooxygenase;
KW Oxidoreductase.
FT CHAIN 1..471
FT /note="Ribulose bisphosphate carboxylase large chain 2"
FT /id="PRO_0000251467"
FT ACT_SITE 168
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT ACT_SITE 287
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 116
FT /ligand="substrate"
FT /note="in homodimeric partner"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 166
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 170
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 194
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 196
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 197
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 288
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 320
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 372
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT SITE 327
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT MOD_RES 194
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
SQ SEQUENCE 471 AA; 51865 MW; 3568693BCFA7BBDD CRC64;
MASKTFDAGV QDYQLTYWTP DYTPLDTDLL ACFKVVPQDG VPREEAAAAV AAESSTGTWT
TVWTDLLTDM EFYKGRCYRI EDVPGDKNAF YAFIAYPLDL FEEGSVVNVL TSLVGNVFGF
KAVRSLRLED LRFPIAFIKT CGGPPAGIQV ERDKLNKYGR PMLGCTIKPK LGLSAKNYGR
AVYECLRGGL DLTKDDENIN SQPFQRWQNR FEFVADAVDK ATAETGERKG HYLNVTAGTV
EEMMKRAEFA KELGQPIIMH DFLTAGFTAN TTLANWCRDN GMLLHIHRAM HAVIDRNPNH
GIHFRVLAKC LRLSGGDHLH TGTVVGKLEG DRASTLGFVD QLREAFVPED RSRGVFFDQD
WGSMPGVMAV ASGGIHVWHM PALVNIFGDD SVLQFGGGTQ GHPGGNAAGA AANRVALEAC
VKARNEGRDL EREGGDILRD AARNSKELAV ALDTWKEIKF EFDTVDKLDV G
