ID SUCD_THETH Reviewed; 288 AA.
AC P09143;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 27-MAR-2024, entry version 135.
DE RecName: Full=Succinate--CoA ligase [GDP-forming] subunit alpha {ECO:0000305|PubMed:22751660};
DE EC=6.2.1.4 {ECO:0000269|PubMed:22751660};
DE AltName: Full=Succinyl-CoA synthetase subunit alpha {ECO:0000255|HAMAP-Rule:MF_01988};
DE Short=SCS-alpha {ECO:0000255|HAMAP-Rule:MF_01988};
GN Name=sucD {ECO:0000255|HAMAP-Rule:MF_01988}; Synonyms=scsA;
OS Thermus thermophilus.
OC Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=B / NCIMB 11247;
RX PubMed=3186449; DOI=10.1093/nar/16.20.9858;
RA Nicholls D.J., Sundaram T.K., Atkinson T., Minton N.P.;
RT "Nucleotide sequence of the succinyl-CoA synthetase alpha-subunit from
RT Thermus aquaticus B.";
RL Nucleic Acids Res. 16:9858-9858(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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 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 [4]
RP X-RAY CRYSTALLOGRAPHY (1.23 ANGSTROMS).
RG RIKEN structural genomics initiative (RSGI);
RT "The crystal structure of succinyl-CoA synthetase from Thermus
RT thermophilus.";
RL Submitted (JUL-2003) to the PDB data bank.
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS), ACTIVE SITE, CATALYTIC ACTIVITY,
RP 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 alpha subunit of the enzyme binds the
CC substrates coenzyme A and phosphate, while succinate binding and
CC nucleotide specificity is provided by the beta subunit (By similarity).
CC Can use either ATP or GTP, but prefers GTP (PubMed:22751660).
CC {ECO:0000255|HAMAP-Rule:MF_01988, 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 PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:22122;
CC Evidence={ECO:0000269|PubMed:22751660};
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; Evidence={ECO:0000269|PubMed:22751660};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:17663;
CC Evidence={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_01988, ECO:0000305|PubMed:22751660}.
CC -!- SUBUNIT: Heterotetramer of two alpha and two beta subunits.
CC {ECO:0000255|HAMAP-Rule:MF_01988, ECO:0000269|PubMed:22751660}.
CC -!- SIMILARITY: Belongs to the succinate/malate CoA ligase alpha subunit
CC family. {ECO:0000255|HAMAP-Rule:MF_01988}.
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DR EMBL; M35832; AAA27504.2; -; Genomic_DNA.
DR EMBL; X56033; CAA39507.1; -; Genomic_DNA.
DR EMBL; X54073; CAA38007.1; -; Genomic_DNA.
DR RefSeq; WP_014509987.1; NZ_LR027517.1.
DR PDB; 1OI7; X-ray; 1.23 A; A=1-288.
DR PDB; 3UFX; X-ray; 2.35 A; A/D/F/H=1-288.
DR PDBsum; 1OI7; -.
DR PDBsum; 3UFX; -.
DR AlphaFoldDB; P09143; -.
DR SMR; P09143; -.
DR UniPathway; UPA00223; UER00999.
DR EvolutionaryTrace; P09143; -.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
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; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR Gene3D; 3.40.50.261; Succinyl-CoA synthetase domains; 1.
DR HAMAP; MF_01988; Succ_CoA_alpha; 1.
DR InterPro; IPR017440; Cit_synth/succinyl-CoA_lig_AS.
DR InterPro; IPR033847; Citrt_syn/SCS-alpha_CS.
DR InterPro; IPR003781; CoA-bd.
DR InterPro; IPR005810; CoA_lig_alpha.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR005811; SUCC_ACL_C.
DR InterPro; IPR016102; Succinyl-CoA_synth-like.
DR NCBIfam; TIGR01019; sucCoAalpha; 1.
DR PANTHER; PTHR11117:SF2; SUCCINATE--COA LIGASE [ADP_GDP-FORMING] SUBUNIT ALPHA, MITOCHONDRIAL; 1.
DR PANTHER; PTHR11117; SUCCINYL-COA LIGASE SUBUNIT ALPHA; 1.
DR Pfam; PF02629; CoA_binding; 1.
DR Pfam; PF00549; Ligase_CoA; 1.
DR PIRSF; PIRSF001553; SucCS_alpha; 1.
DR PRINTS; PR01798; SCOASYNTHASE.
DR SMART; SM00881; CoA_binding; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
DR SUPFAM; SSF52210; Succinyl-CoA synthetase domains; 1.
DR PROSITE; PS01216; SUCCINYL_COA_LIG_1; 1.
DR PROSITE; PS00399; SUCCINYL_COA_LIG_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Ligase; Nucleotide-binding; Tricarboxylic acid cycle.
FT CHAIN 1..288
FT /note="Succinate--CoA ligase [GDP-forming] subunit alpha"
FT /id="PRO_0000102807"
FT ACT_SITE 246
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988,
FT ECO:0000269|PubMed:22751660"
FT BINDING 16..19
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988"
FT BINDING 42
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988"
FT BINDING 95..97
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988"
FT BINDING 158
FT /ligand="substrate"
FT /ligand_note="ligand shared with subunit beta"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988"
FT CONFLICT 130..132
FT /note="EET -> HLP (in Ref. 1; AAA27504)"
FT /evidence="ECO:0000305"
FT CONFLICT 157..158
FT /note="TY -> RH (in Ref. 1; AAA27504)"
FT /evidence="ECO:0000305"
FT CONFLICT 183..185
FT /note="IGT -> RRL (in Ref. 1; AAA27504)"
FT /evidence="ECO:0000305"
FT STRAND 9..13
FT /evidence="ECO:0007829|PDB:1OI7"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 18..30
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 33..38
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 50..55
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 56..62
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 74..86
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 101..114
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:1OI7"
FT TURN 129..131
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 132..137
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 144..152
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 154..166
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 171..176
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 187..195
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 202..207
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 213..224
FT /evidence="ECO:0007829|PDB:1OI7"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:1OI7"
FT TURN 235..237
FT /evidence="ECO:0007829|PDB:3UFX"
FT HELIX 258..268
FT /evidence="ECO:0007829|PDB:1OI7"
FT HELIX 276..287
FT /evidence="ECO:0007829|PDB:1OI7"
SQ SEQUENCE 288 AA; 29822 MW; 243A68469E78AF68 CRC64;
MILVNRETRV LVQGITGREG QFHTKQMLDY GTKIVAGVTP GKGGTEVLGV PVYDTVKEAV
AHHEVDASII FVPAPAAADA ALEAAHAGIP LIVLITEGIP TLDMVRAVEE IKALGSRLIG
GNCPGIISAE ETKIGIMPGH VFKRGRVGII SRSGTLTYEA AAALSQAGLG TTTTVGIGGD
PVIGTTFKDL LPLFNEDPET EAVVLIGEIG GSDEEEAAAW VKDHMKKPVV GFIGGRSAPK
GKRMGHAGAI IMGNVGTPES KLRAFAEAGI PVADTIDEIV ELVKKALG
//
