CARB_ORYSJ
ID CARB_ORYSJ Reviewed; 1172 AA.
AC B9EXM2; Q0JLU1;
DT 24-JUL-2013, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Carbamoyl-phosphate synthase large chain, chloroplastic;
DE EC=6.3.5.5;
DE AltName: Full=Carbamoyl-phosphate synthetase ammonia chain;
DE Flags: Precursor;
GN Name=CARB; OrderedLocusNames=Os01g0570700, LOC_Os01g38970;
GN ORFNames=OsJ_02282;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 847-1172.
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Involved in arginine biosynthesis. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP +
CC carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate;
CC Xref=Rhea:RHEA:18633, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17544, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58228, ChEBI:CHEBI:58359,
CC ChEBI:CHEBI:456216; EC=6.3.5.5;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00409};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00409};
CC Note=Binds 4 Mg(2+) or Mn(2+) ions per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00409};
CC -!- PATHWAY: Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl
CC phosphate from bicarbonate: step 1/1.
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC (S)-dihydroorotate from bicarbonate: step 1/3.
CC -!- SUBUNIT: Composed of two chains; the small (or glutamine) chain
CC promotes the hydrolysis of glutamine to ammonia, which is used by the
CC large (or ammonia) chain to synthesize carbamoyl phosphate.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the CarB family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF05287.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP003334; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP008207; BAF05287.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000138; EEE54835.1; -; Genomic_DNA.
DR EMBL; AK061023; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015617454.1; XM_015761968.1.
DR AlphaFoldDB; B9EXM2; -.
DR SMR; B9EXM2; -.
DR STRING; 4530.OS01T0570700-01; -.
DR PaxDb; B9EXM2; -.
DR PRIDE; B9EXM2; -.
DR GeneID; 4326346; -.
DR KEGG; osa:4326346; -.
DR eggNOG; KOG0370; Eukaryota.
DR HOGENOM; CLU_000513_3_4_1; -.
DR OrthoDB; 273358at2759; -.
DR PlantReactome; R-OSA-1119263; Arginine biosynthesis.
DR PlantReactome; R-OSA-1119622; Arginine biosynthesis II (acetyl cycle).
DR UniPathway; UPA00068; UER00171.
DR UniPathway; UPA00070; UER00115.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; B9EXM2; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004088; F:carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006526; P:arginine biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006541; P:glutamine metabolic process; IBA:GO_Central.
DR GO; GO:0006807; P:nitrogen compound metabolic process; IBA:GO_Central.
DR CDD; cd01424; MGS_CPS_II; 1.
DR Gene3D; 1.10.1030.10; -; 1.
DR Gene3D; 3.30.1490.20; -; 1.
DR Gene3D; 3.40.50.1380; -; 1.
DR HAMAP; MF_01210_A; CPSase_L_chain_A; 1.
DR HAMAP; MF_01210_B; CPSase_L_chain_B; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR006275; CarbamoylP_synth_lsu.
DR InterPro; IPR005480; CarbamoylP_synth_lsu_oligo.
DR InterPro; IPR036897; CarbamoylP_synth_lsu_oligo_sf.
DR InterPro; IPR005479; CbamoylP_synth_lsu-like_ATP-bd.
DR InterPro; IPR005483; CbamoylP_synth_lsu_CPSase_dom.
DR InterPro; IPR011607; MGS-like_dom.
DR InterPro; IPR036914; MGS-like_dom_sf.
DR InterPro; IPR033937; MGS_CPS_CarB.
DR InterPro; IPR016185; PreATP-grasp_dom_sf.
DR Pfam; PF02786; CPSase_L_D2; 2.
DR Pfam; PF02787; CPSase_L_D3; 1.
DR Pfam; PF02142; MGS; 1.
DR PRINTS; PR00098; CPSASE.
DR SMART; SM01096; CPSase_L_D3; 1.
DR SMART; SM00851; MGS; 1.
DR SUPFAM; SSF48108; SSF48108; 1.
DR SUPFAM; SSF52335; SSF52335; 1.
DR SUPFAM; SSF52440; SSF52440; 2.
DR TIGRFAMs; TIGR01369; CPSaseII_lrg; 1.
DR PROSITE; PS50975; ATP_GRASP; 2.
DR PROSITE; PS00866; CPSASE_1; 2.
DR PROSITE; PS00867; CPSASE_2; 2.
DR PROSITE; PS51855; MGS; 1.
PE 2: Evidence at transcript level;
KW Amino-acid biosynthesis; Arginine biosynthesis; ATP-binding; Chloroplast;
KW Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding; Plastid;
KW Pyrimidine biosynthesis; Reference proteome; Repeat; Transit peptide.
FT TRANSIT 1..50
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 51..1172
FT /note="Carbamoyl-phosphate synthase large chain,
FT chloroplastic"
FT /id="PRO_0000423077"
FT DOMAIN 203..399
FT /note="ATP-grasp 1"
FT DOMAIN 761..954
FT /note="ATP-grasp 2"
FT DOMAIN 1021..1162
FT /note="MGS-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01202"
FT REGION 1..37
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..17
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 230..287
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 356
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 370
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 370
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 372
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 787..844
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 912
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 925
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 925
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 927
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
SQ SEQUENCE 1172 AA; 127767 MW; 5DEF305423F90C63 CRC64;
MATSLSSAPT QLRPSPSPSH HRLLHRSSLL PFPRRHHHRR RRCGALSIAR ASASAKDGVT
VRRFPAAPTE GGRLAGVRKI MILGAGPIVI GQACEFDYSG TQACKALAEE GYEVVLVNSN
PATIMTDPDL AHRTYIGPMT PPLVERIIAA ERPDALLPTM GGQTALNLAV SLADSGALDR
LGVRLIGASL PAIRAAEDRQ LFKQAMDRIG LKTPPSGIGT TLEECISIAE DIGEFPLIVR
PAFTLGGTGG GIAYNRAEFE DICRAGLAAS HTQQVLVEKS LLGWKEYELE VMRDMADNVV
IICSIENIDP MGVHTGDSIT VAPAQTLTDK EYQRLRDYSV AIIREIGVEC GGSNVQFAVN
PADGEVMVIE MNPRVSRSSA LASKATGFPI AKMAAKLSVG YTLDQIPNDI TKKTPASFEP
SIDYVVTKIP RFAFEKFPGS EPVLTTQMKS VGEAMALGRT FQESFQKAVR SLETGFAGWG
CAPIKELDWD WEKLKYSLRV PNPDRIHAIY AAFKKGMRIQ DIHEISFIDK WFLTELKELV
DVEQFLISRG LDQLSKDDFY QVKRRGFSDT QIAFATSSSE TDVRLRRLAL EVAPTYKRVD
TCAAEFEANT PYMYSSYEYE CESVPTNKKK VLILGGGPNR IGQGIEFDYC CCHASFALRE
AGYETIMMNS NPETVSTDYD TSDRLYFEPL TVEDVTNVID LERPDGIIVQ FGGQTPLKLA
LPIQQYLEDK KLVSASGTGL VKIWGTSPDS IDAAEDRKRF NAILEELGIE QPKGGIARSE
SDALSIASEV GYPVVVRPSY VLGGRAMEIV YNDEKLIKYL ATAVQVDPER PVLVDKYLID
AIEIDVDALA DSVGNVVIGG IMEHIEQAGI HSGDSACSLP TRTVSAKCLD IIRSWTTKLA
KRLNVCGLMN CQYAITTSGE VFLLEANPRA SRTVPFVSKA IGHPLAKYAS LVMSGVTLPE
LGYTQEVVPK HVSVKEAVLP FEKFQGCDIL LGPEMRSTGE VMGIDYEFSG AFAKAQIAAG
QKLPLNGTVF LSLNDLTKRH LAEIGRGFRE LGFNIIATSG TAKVLQLEGI PVEPVLKIHE
GRPNARDMLK NGQIQVMVIT SSGDALDSKD GLQLRRLALA YKVPIITTVD GARATIDAIK
SLKNKSIETL ALQDYFQTTD ASQNLQAAQS AS
