ID SUCB_ORYSJ Reviewed; 422 AA.
AC Q6K9N6; Q0DZG1;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 27-MAR-2024, entry version 129.
DE RecName: Full=Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial {ECO:0000255|HAMAP-Rule:MF_03219};
DE EC=6.2.1.5 {ECO:0000255|HAMAP-Rule:MF_03219};
DE AltName: Full=Succinyl-CoA synthetase beta chain {ECO:0000255|HAMAP-Rule:MF_03219};
DE Short=SCS-beta {ECO:0000255|HAMAP-Rule:MF_03219};
DE Flags: Precursor;
GN OrderedLocusNames=Os02g0621700, LOC_Os02g40830;
GN ORFNames=OJ1234_B11.18, OsJ_07569 {ECO:0000312|EMBL:EAZ23853.1};
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=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 [2]
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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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).
RN [6]
RP PROTEIN SEQUENCE [LARGE SCALE ANALYSIS] OF 28-34, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC STRAIN=cv. Nipponbare;
RX PubMed=16758443; DOI=10.1002/pmic.200600043;
RA Nozu Y., Tsugita A., Kamijo K.;
RT "Proteomic analysis of rice leaf, stem and root tissues during growth
RT course.";
RL Proteomics 6:3665-3670(2006).
CC -!- FUNCTION: Succinyl-CoA synthetase functions in the citric acid cycle
CC (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP
CC and thus represents the only step of substrate-level phosphorylation in
CC the TCA. The beta subunit provides nucleotide specificity of the enzyme
CC and binds the substrate succinate, while the binding sites for coenzyme
CC A and phosphate are found in the alpha subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03219}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + succinate = ADP + phosphate + succinyl-CoA;
CC Xref=Rhea:RHEA:17661, ChEBI:CHEBI:30031, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57287, ChEBI:CHEBI:57292,
CC ChEBI:CHEBI:456216; EC=6.2.1.5; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03219};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03219};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_03219};
CC -!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; succinate
CC from succinyl-CoA (ligase route): step 1/1. {ECO:0000255|HAMAP-
CC Rule:MF_03219}.
CC -!- SUBUNIT: Heterodimer of an alpha and a beta subunit.
CC {ECO:0000255|HAMAP-Rule:MF_03219}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03219}.
CC -!- SIMILARITY: Belongs to the succinate/malate CoA ligase beta subunit
CC family. {ECO:0000255|HAMAP-Rule:MF_03219}.
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DR EMBL; AP004053; BAD21546.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF09377.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS79828.1; -; Genomic_DNA.
DR EMBL; CM000139; EAZ23853.1; -; Genomic_DNA.
DR EMBL; AK101006; BAG94878.1; -; mRNA.
DR RefSeq; XP_015625812.1; XM_015770326.1.
DR AlphaFoldDB; Q6K9N6; -.
DR SMR; Q6K9N6; -.
DR STRING; 39947.Q6K9N6; -.
DR PaxDb; 39947-Q6K9N6; -.
DR EnsemblPlants; Os02t0621700-01; Os02t0621700-01; Os02g0621700.
DR GeneID; 4330016; -.
DR Gramene; Os02t0621700-01; Os02t0621700-01; Os02g0621700.
DR KEGG; osa:4330016; -.
DR eggNOG; KOG2799; Eukaryota.
DR HOGENOM; CLU_037430_0_0_1; -.
DR InParanoid; Q6K9N6; -.
DR OMA; ITACDEV; -.
DR OrthoDB; 1384037at2759; -.
DR PlantReactome; R-OSA-1119533; TCA cycle (plant).
DR UniPathway; UPA00223; UER00999.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; Q6K9N6; baseline and differential.
DR Genevisible; Q6K9N6; OS.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0042709; C:succinate-CoA ligase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004775; F:succinate-CoA ligase (ADP-forming) activity; IBA:GO_Central.
DR GO; GO:0006104; P:succinyl-CoA metabolic process; IBA:GO_Central.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IBA:GO_Central.
DR Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1.
DR Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 1.
DR Gene3D; 3.40.50.261; Succinyl-CoA synthetase domains; 1.
DR HAMAP; MF_00558; Succ_CoA_beta; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013650; ATP-grasp_succ-CoA_synth-type.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR017866; Succ-CoA_synthase_bsu_CS.
DR InterPro; IPR005811; SUCC_ACL_C.
DR InterPro; IPR005809; Succ_CoA_ligase-like_bsu.
DR InterPro; IPR016102; Succinyl-CoA_synth-like.
DR NCBIfam; TIGR01016; sucCoAbeta; 1.
DR PANTHER; PTHR11815:SF10; SUCCINATE--COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL; 1.
DR PANTHER; PTHR11815; SUCCINYL-COA SYNTHETASE BETA CHAIN; 1.
DR Pfam; PF08442; ATP-grasp_2; 1.
DR Pfam; PF00549; Ligase_CoA; 1.
DR PIRSF; PIRSF001554; SucCS_beta; 1.
DR SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1.
DR SUPFAM; SSF52210; Succinyl-CoA synthetase domains; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
DR PROSITE; PS01217; SUCCINYL_COA_LIG_3; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Direct protein sequencing; Ligase; Magnesium; Metal-binding;
KW Mitochondrion; Nucleotide-binding; Reference proteome; Transit peptide;
KW Tricarboxylic acid cycle.
FT TRANSIT 1..27
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:16758443"
FT CHAIN 28..422
FT /note="Succinate--CoA ligase [ADP-forming] subunit beta,
FT mitochondrial"
FT /id="PRO_0000247501"
FT DOMAIN 36..279
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 75
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 82..84
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 142
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 234
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 299
FT /ligand="substrate"
FT /ligand_note="ligand shared with subunit alpha"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
FT BINDING 356..358
FT /ligand="substrate"
FT /ligand_note="ligand shared with subunit alpha"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03219"
SQ SEQUENCE 422 AA; 45091 MW; D6E3792586394BB7 CRC64;
MVRGSLGKLA SRALSVAGKW QHQQLRRLNI HEYQGAELMG KYGINVPRGA AAGSVEEVKN
TLKNVFPSEK EIVVKSQILA GGRGLGTFKS GLQGGVHIVK AEEAESLAAK MLGQILVTKQ
TGPQGKIVSK VYLCEKLSLV NEMYFAITLD RNTAGPLIIA CSKGGTSIED LAEKYPDMII
KVPIDVFKGI TDDDAAKVVD GLAPKTADRQ SSIEQIKKLY ELFCKSDCTL LEINPLAETA
DNKLVAADAK LNFDDNAAFR QKEIFAMRDT TQEDPREVAA AKADLNYIGL DGEIGCMVNG
AGLAMATMDI IKLHGGTPAN FLDVGGSASE GQVVEAFKIL TSDDRVKAIL VNIFGGIMKC
DVIASGIVNA AKQVDLKVPV VVRLEGTNVD QGKRILKESG MTLITAEDLD DAAEKAVKAS
VK
//
