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Database: UniProt
Entry: P25126
LinkDB: P25126
Original site: P25126 
ID   SUCC_THETH              Reviewed;         378 AA.
AC   P25126;
DT   01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1992, sequence version 1.
DT   05-DEC-2018, entry version 95.
DE   RecName: Full=Succinate--CoA ligase [GDP-forming] subunit beta {ECO:0000305|PubMed:22751660};
DE            EC=6.2.1.4 {ECO:0000269|PubMed:22751660};
DE   AltName: Full=Succinyl-CoA synthetase subunit beta {ECO:0000255|HAMAP-Rule:MF_00558};
DE            Short=SCS-beta {ECO:0000255|HAMAP-Rule:MF_00558};
GN   Name=sucC {ECO:0000255|HAMAP-Rule:MF_00558}; Synonyms=scsB;
OS   Thermus thermophilus.
OC   Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae;
OC   Thermus.
OX   NCBI_TaxID=274;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 33923 / DSM 674 / AT-62;
RX   PubMed=2034208; DOI=10.1007/BF00273580;
RA   Nishiyama M., Horinouchi S., Beppu T.;
RT   "Characterization of an operon encoding succinyl-CoA synthetase and
RT   malate dehydrogenase from Thermus flavus AT-62 and its expression in
RT   Escherichia coli.";
RL   Mol. Gen. Genet. 226:1-9(1991).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 350-378.
RC   STRAIN=B / NCIB 11247;
RX   PubMed=2204576; DOI=10.1016/0378-1097(90)90093-6;
RA   Nicholls D.J., Sundaram T.K., Atkinson T., Minton N.P.;
RT   "Cloning and nucleotide sequences of the mdh and sucD genes from
RT   Thermus aquaticus B.";
RL   FEMS Microbiol. Lett. 58:7-14(1990).
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH GDP AND
RP   MANGANESE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP   SUBUNIT.
RX   PubMed=22751660; DOI=10.1107/S0907444912010852;
RA   Joyce M.A., Hayakawa K., Wolodko W.T., Fraser M.E.;
RT   "Biochemical and structural characterization of the GTP-preferring
RT   succinyl-CoA synthetase from Thermus aquaticus.";
RL   Acta Crystallogr. D 68:751-762(2012).
CC   -!- FUNCTION: Succinyl-CoA synthetase functions in the citric acid
CC       cycle (TCA), coupling the hydrolysis of succinyl-CoA to the
CC       synthesis of either ATP or GTP and thus represents the only step
CC       of substrate-level phosphorylation in the TCA. The beta subunit
CC       provides nucleotide specificity of the enzyme and binds the
CC       substrate succinate, while the binding sites for coenzyme A and
CC       phosphate are found in the alpha subunit (By similarity). Can use
CC       either ATP or GTP, but prefers GTP (PubMed:22751660).
CC       {ECO:0000255|HAMAP-Rule:MF_00558, ECO:0000269|PubMed:22751660}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=CoA + GTP + succinate = GDP + phosphate + succinyl-CoA;
CC         Xref=Rhea:RHEA:22120, ChEBI:CHEBI:30031, ChEBI:CHEBI:37565,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:57287, ChEBI:CHEBI:57292,
CC         ChEBI:CHEBI:58189; EC=6.2.1.4;
CC         Evidence={ECO:0000269|PubMed:22751660};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00558,
CC         ECO:0000269|PubMed:22751660};
CC       Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-
CC       Rule:MF_00558, ECO:0000269|PubMed:22751660};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=121 uM for ATP {ECO:0000269|PubMed:22751660};
CC         KM=24 uM for GTP {ECO:0000269|PubMed:22751660};
CC         KM=1.4 mM for succinate {ECO:0000269|PubMed:22751660};
CC         KM=5.5 uM for CoA {ECO:0000269|PubMed:22751660};
CC       pH dependence:
CC         Optimum pH is 8.0-8.4. {ECO:0000269|PubMed:22751660};
CC   -!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle;
CC       succinate from succinyl-CoA (ligase route): step 1/1.
CC       {ECO:0000255|HAMAP-Rule:MF_00558, ECO:0000305|PubMed:22751660}.
CC   -!- SUBUNIT: Heterotetramer of two alpha and two beta subunits.
CC       {ECO:0000255|HAMAP-Rule:MF_00558, ECO:0000269|PubMed:22751660}.
CC   -!- SIMILARITY: Belongs to the succinate/malate CoA ligase beta
CC       subunit family. {ECO:0000255|HAMAP-Rule:MF_00558}.
DR   EMBL; X54073; CAA38006.1; -; Genomic_DNA.
DR   EMBL; X56033; CAA39506.1; -; Genomic_DNA.
DR   PDB; 3UFX; X-ray; 2.35 A; B/E/G/I=1-378.
DR   PDBsum; 3UFX; -.
DR   ProteinModelPortal; P25126; -.
DR   SMR; P25126; -.
DR   PRIDE; P25126; -.
DR   eggNOG; ENOG4105CMV; Bacteria.
DR   eggNOG; COG0045; LUCA.
DR   UniPathway; UPA00223; UER00999.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0004775; F:succinate-CoA ligase (ADP-forming) activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0004776; F:succinate-CoA ligase (GDP-forming) activity; IEA:UniProtKB-EC.
DR   GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.30.1490.20; -; 1.
DR   Gene3D; 3.40.50.261; -; 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; IPR005811; CoA_ligase.
DR   InterPro; IPR017866; Succ-CoA_synthase_bsu_CS.
DR   InterPro; IPR005809; Succ_CoA_synthase_bsu.
DR   InterPro; IPR016102; Succinyl-CoA_synth-like.
DR   PANTHER; PTHR11815; PTHR11815; 1.
DR   Pfam; PF08442; ATP-grasp_2; 1.
DR   Pfam; PF00549; Ligase_CoA; 1.
DR   PIRSF; PIRSF001554; SucCS_beta; 1.
DR   SUPFAM; SSF52210; SSF52210; 1.
DR   TIGRFAMs; TIGR01016; sucCoAbeta; 1.
DR   PROSITE; PS50975; ATP_GRASP; 1.
DR   PROSITE; PS01217; SUCCINYL_COA_LIG_3; 1.
PE   1: Evidence at protein level;
KW   3D-structure; GTP-binding; Ligase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Tricarboxylic acid cycle.
FT   CHAIN         1    378       Succinate--CoA ligase [GDP-forming]
FT                                subunit beta.
FT                                /FTId=PRO_0000102871.
FT   DOMAIN        9    235       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00558}.
FT   NP_BIND      52     54       GTP. {ECO:0000269|PubMed:22751660}.
FT   REGION      312    314       Substrate binding; shared with subunit
FT                                alpha. {ECO:0000255|HAMAP-Rule:MF_00558}.
FT   METAL       190    190       Magnesium. {ECO:0000255|HAMAP-
FT                                Rule:MF_00558,
FT                                ECO:0000269|PubMed:22751660}.
FT   METAL       204    204       Magnesium. {ECO:0000255|HAMAP-
FT                                Rule:MF_00558,
FT                                ECO:0000269|PubMed:22751660}.
FT   BINDING      45     45       GTP. {ECO:0000269|PubMed:22751660}.
FT   BINDING      94     94       GTP; via amide nitrogen and carbonyl
FT                                oxygen. {ECO:0000269|PubMed:22751660}.
FT   BINDING      99     99       GTP. {ECO:0000269|PubMed:22751660}.
FT   BINDING     255    255       Substrate; shared with subunit alpha.
FT                                {ECO:0000255|HAMAP-Rule:MF_00558}.
FT   CONFLICT    357    357       V -> I (in Ref. 2; CAA39506).
FT                                {ECO:0000305}.
FT   HELIX         5     14       {ECO:0000244|PDB:3UFX}.
FT   STRAND       22     27       {ECO:0000244|PDB:3UFX}.
FT   HELIX        28     38       {ECO:0000244|PDB:3UFX}.
FT   STRAND       42     46       {ECO:0000244|PDB:3UFX}.
FT   STRAND       49     51       {ECO:0000244|PDB:3UFX}.
FT   TURN         53     57       {ECO:0000244|PDB:3UFX}.
FT   STRAND       59     64       {ECO:0000244|PDB:3UFX}.
FT   HELIX        65     75       {ECO:0000244|PDB:3UFX}.
FT   STRAND       88     92       {ECO:0000244|PDB:3UFX}.
FT   STRAND       96    107       {ECO:0000244|PDB:3UFX}.
FT   TURN        108    111       {ECO:0000244|PDB:3UFX}.
FT   STRAND      112    119       {ECO:0000244|PDB:3UFX}.
FT   HELIX       125    131       {ECO:0000244|PDB:3UFX}.
FT   HELIX       133    135       {ECO:0000244|PDB:3UFX}.
FT   STRAND      137    140       {ECO:0000244|PDB:3UFX}.
FT   TURN        143    145       {ECO:0000244|PDB:3UFX}.
FT   HELIX       149    159       {ECO:0000244|PDB:3UFX}.
FT   HELIX       165    181       {ECO:0000244|PDB:3UFX}.
FT   STRAND      184    195       {ECO:0000244|PDB:3UFX}.
FT   STRAND      200    204       {ECO:0000244|PDB:3UFX}.
FT   STRAND      206    209       {ECO:0000244|PDB:3UFX}.
FT   HELIX       211    216       {ECO:0000244|PDB:3UFX}.
FT   HELIX       218    221       {ECO:0000244|PDB:3UFX}.
FT   HELIX       224    227       {ECO:0000244|PDB:3UFX}.
FT   HELIX       231    238       {ECO:0000244|PDB:3UFX}.
FT   STRAND      242    245       {ECO:0000244|PDB:3UFX}.
FT   STRAND      247    256       {ECO:0000244|PDB:3UFX}.
FT   HELIX       257    269       {ECO:0000244|PDB:3UFX}.
FT   STRAND      274    279       {ECO:0000244|PDB:3UFX}.
FT   HELIX       286    297       {ECO:0000244|PDB:3UFX}.
FT   STRAND      304    316       {ECO:0000244|PDB:3UFX}.
FT   HELIX       317    327       {ECO:0000244|PDB:3UFX}.
FT   TURN        328    330       {ECO:0000244|PDB:3UFX}.
FT   STRAND      336    343       {ECO:0000244|PDB:3UFX}.
FT   HELIX       345    351       {ECO:0000244|PDB:3UFX}.
FT   TURN        352    354       {ECO:0000244|PDB:3UFX}.
FT   STRAND      355    359       {ECO:0000244|PDB:3UFX}.
FT   HELIX       363    372       {ECO:0000244|PDB:3UFX}.
SQ   SEQUENCE   378 AA;  40603 MW;  39988244C1393C5D CRC64;
     MNLHEYQAKE ILARYGVPVP PGKVAYTPEE AKRIAEEFGK RVVIKAQVHV GGRGKAGGVK
     LADTPQEAYE KAQAILGMNI KGLTVKKVLV AEAVDIAKEY YAGLILDRAK KRVVLMLSKE
     GGVDIEEVAA ERPEAIHKFW IDPHKGFRPF EAREMVKRAG LEGNLNKLAQ VLVALYRAYE
     GVDASIAEIN PLVVTTDGGI VAADAKIVLD DNALFRHPDL AELREVEAEH PLEVEASNYG
     FAYVKLDGNI GIIGNGAGLV MYTLDLVNRV GGKPANFLDI GGGAKADVVY NALKVVLKDP
     DVKGVFINIF GGITRADEVA KGVIRALEEG LLTKPVVMRV AGTAEEEAKK LLEGKPVYMY
     PTSIEAAKAI VAMVGGAA
//
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