SUCC_THETH
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 03-AUG-2022, entry version 104.
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; 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 malate
RT dehydrogenase from Thermus flavus AT-62 and its expression in Escherichia
RT coli.";
RL Mol. Gen. Genet. 226:1-9(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 350-378.
RC STRAIN=B / NCIMB 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 Thermus
RT aquaticus B.";
RL FEMS Microbiol. Lett. 58:7-14(1990).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH GDP AND MANGANESE,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND 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 cycle
CC (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of
CC either ATP or GTP and thus represents the only step of substrate-level
CC phosphorylation in the TCA. The beta subunit provides nucleotide
CC specificity of the enzyme and binds the substrate succinate, while the
CC binding sites for coenzyme A and phosphate are found in the alpha
CC subunit (By similarity). Can use either ATP or GTP, but prefers GTP
CC (PubMed:22751660). {ECO:0000255|HAMAP-Rule:MF_00558,
CC 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-Rule:MF_00558,
CC 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; succinate
CC from succinyl-CoA (ligase route): step 1/1. {ECO:0000255|HAMAP-
CC 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 subunit
CC family. {ECO:0000255|HAMAP-Rule:MF_00558}.
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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 AlphaFoldDB; P25126; -.
DR SMR; P25126; -.
DR UniPathway; UPA00223; UER00999.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProt.
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
FT /note="Succinate--CoA ligase [GDP-forming] subunit beta"
FT /id="PRO_0000102871"
FT DOMAIN 9..235
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00558"
FT BINDING 45
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:22751660"
FT BINDING 52..54
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:22751660"
FT BINDING 94
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:22751660"
FT BINDING 99
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:22751660"
FT BINDING 190
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00558,
FT ECO:0000269|PubMed:22751660"
FT BINDING 204
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00558,
FT ECO:0000269|PubMed:22751660"
FT BINDING 255
FT /ligand="substrate"
FT /ligand_note="ligand shared with subunit alpha"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00558"
FT BINDING 312..314
FT /ligand="substrate"
FT /ligand_note="ligand shared with subunit alpha"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00558"
FT CONFLICT 357
FT /note="V -> I (in Ref. 2; CAA39506)"
FT /evidence="ECO:0000305"
FT HELIX 5..14
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 22..27
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 28..38
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 49..51
FT /evidence="ECO:0007829|PDB:3UFX"
FT TURN 53..57
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 65..75
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 88..92
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 96..107
FT /evidence="ECO:0007829|PDB:3UFX"
FT TURN 108..111
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 112..119
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 125..131
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:3UFX"
FT TURN 143..145
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 149..159
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 165..181
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 184..195
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 200..204
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 211..216
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 218..221
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 224..227
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 231..238
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 242..245
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 247..256
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 257..269
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 274..279
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 286..297
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 304..316
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 317..327
FT /evidence="ECO:0007829|PDB:3UFX"
FT TURN 328..330
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 336..343
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 345..351
FT /evidence="ECO:0007829|PDB:3UFX"
FT TURN 352..354
FT /evidence="ECO:0007829|PDB:3UFX"
FT STRAND 355..359
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 363..372
FT /evidence="ECO:0007829|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
