RBL1B_HYDMR
ID RBL1B_HYDMR Reviewed; 471 AA.
AC Q59460; Q75W40;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 97.
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};
GN Name=cbbL2 {ECO:0000255|HAMAP-Rule:MF_01338};
GN Synonyms=cbbL-2 {ECO:0000303|PubMed:9531639};
OS Hydrogenovibrio marinus.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales;
OC Piscirickettsiaceae; Hydrogenovibrio.
OX NCBI_TaxID=28885;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 11271 / JCM 7688 / MH-110;
RX PubMed=9531639; DOI=10.1007/s002030050584;
RA Nishihara H., Yaguchi T., Chung S.-Y., Suzuki K., Yanagi M., Yamasato K.,
RA Kodama T., Igarashi Y.;
RT "Phylogenetic position of an obligately chemoautotrophic, marine hydrogen-
RT oxidizing bacterium, Hydrogenovibrio marinus, on the basis of 16S rRNA gene
RT sequences and two form I RuBisCO gene sequences.";
RL Arch. Microbiol. 169:364-368(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], POSSIBLE SUBCELLULAR LOCATION, AND
RP INDUCTION OF EXPRESSION BY CO(2) IN H.MARINUS.
RC STRAIN=DSM 11271 / JCM 7688 / MH-110;
RX PubMed=15317772; DOI=10.1128/jb.186.17.5685-5691.2004;
RA Yoshizawa Y., Toyoda K., Arai H., Ishii M., Igarashi Y.;
RT "CO2-responsive expression and gene organization of three ribulose-1,5-
RT bisphosphate carboxylase/oxygenase enzymes and carboxysomes in
RT Hydrogenovibrio marinus strain MH-110.";
RL J. Bacteriol. 186:5685-5691(2004).
RN [3]
RP CHARACTERIZATION IN E.COLI, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RC STRAIN=DSM 11271 / JCM 7688 / MH-110;
RX DOI=10.1016/S0922-338X(97)86759-1;
RA Hayashi N.R., Oguni A., Yaguchi T., Chung S.-Y., Nishihara H., Kodama T.,
RA Igarashi Y.;
RT "Different properties of gene products of three sets ribulose 1,5-
RT bisphosphate carboxylase/oxygenase from a marine obligately autotrophic
RT hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110.";
RL J. Ferment. Bioeng. 85:150-155(1998).
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. {ECO:0000269|Ref.3}.
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|Ref.3};
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 ECO:0000269|Ref.3};
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 Vmax=2.6 umol/min/mg enzyme with CO(2) as substrate, expressed in
CC E.coli {ECO:0000269|Ref.3};
CC Note=The CO(2)/O(2) specificity factor (tau) is 33.1.
CC {ECO:0000269|Ref.3};
CC -!- SUBUNIT: Heterohexadecamer of 8 large chains and 8 small chains.
CC {ECO:0000269|Ref.3, ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Carboxysome {ECO:0000305|PubMed:15317772}.
CC Note=This bacterium makes alpha-type carboxysome. {ECO:0000305}.
CC -!- INDUCTION: Both mRNA and protein accumulate at 0.15% and 0.03% CO(2),
CC but not at 15% or 2% CO(2) (at protein level).
CC {ECO:0000269|PubMed:15317772}.
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,
CC ECO:0000305|PubMed:9531639}.
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DR EMBL; D43622; BAA07731.1; -; Genomic_DNA.
DR EMBL; AB122070; BAD15312.1; -; Genomic_DNA.
DR RefSeq; WP_029910957.1; NZ_JMIU01000001.1.
DR AlphaFoldDB; Q59460; -.
DR SMR; Q59460; -.
DR STRING; 28885.EI16_06350; -.
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_0000062625"
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"
FT CONFLICT 73
FT /note="F -> Y (in Ref. 2; BAD15312)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 471 AA; 52005 MW; BAD462E46451AD60 CRC64;
MASKTFDAGV QDYQLTYWTP DYTPLDTDLL ACFKVVPQEG VPREEAAAAV AAESSTGTWT
TVWTDLLTDM EFFKGRAYRI EDVPGDKNAF YAFIAYPLDL FEEGSVVNVL TSLVGNVFGF
KAVRSLRLED LRFPIAFIKT CGGPPSGIQV ERDKLNKYGR PMLGCTIKPK LGLSAKNYGR
AVYECLRGGL DLTKDDENIN SQPFQRWRDR FEFVAEAVDK ATAETGERKG HYLNVTAGTV
EEMMKRAEFA KELGQPIIMH DFLTAGFTAN TTLANWCREN GMLLHIHRAM HAVIDRNPLH
GIHFRVLAKC LRLSGGDHLH TGTVVGKLEG DRASTLGFVD QLRESFVPED RSRGVFFDQD
WGSMPGVMAV ASGGIHVWHM PALVNIFGDD SVLQFGGGTQ GHPGGNAAGA AANRVALEAC
VKARNEGRDL EREGGDILRE AARTSKELAV ALETWKEIKF EFDTVDKLDV Q
