SUCD_ECOLI
ID SUCD_ECOLI Reviewed; 289 AA.
AC P0AGE9; P07459;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Succinate--CoA ligase [ADP-forming] subunit alpha {ECO:0000255|HAMAP-Rule:MF_01988};
DE EC=6.2.1.5 {ECO:0000255|HAMAP-Rule:MF_01988, ECO:0000269|PubMed:10353839};
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};
GN OrderedLocusNames=b0729, JW0718;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3002435; DOI=10.1021/bi00343a031;
RA Buck D., Spencer M.E., Guest J.R.;
RT "Primary structure of the succinyl-CoA synthetase of Escherichia coli.";
RL Biochemistry 24:6245-6252(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 173-289.
RX PubMed=2548486; DOI=10.1042/bj2600737;
RA Buck D., Guest J.R.;
RT "Overexpression and site-directed mutagenesis of the succinyl-CoA
RT synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that
RT is adjacent to the suc operon.";
RL Biochem. J. 260:737-747(1989).
RN [6]
RP PROTEIN SEQUENCE OF 2-20.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP PROTEIN SEQUENCE OF 2-12.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F.;
RL Submitted (FEB-1996) to UniProtKB.
RN [8]
RP PHOSPHORYLATION, AND PROTEIN SEQUENCE OF 2-11.
RC STRAIN=E2348/69 / EPEC / MAR001;
RX PubMed=7783627; DOI=10.1111/j.1365-2958.1995.tb02270.x;
RA Freestone P., Grant S., Toth I., Norris V.;
RT "Identification of phosphoproteins in Escherichia coli.";
RL Mol. Microbiol. 15:573-580(1995).
RN [9]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=10353839; DOI=10.1021/bi990527s;
RA Joyce M.A., Fraser M.E., Brownie E.R., James M.N., Bridger W.A.,
RA Wolodko W.T.;
RT "Probing the nucleotide-binding site of Escherichia coli succinyl-CoA
RT synthetase.";
RL Biochemistry 38:7273-7283(1999).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUCC AND COENZYME A.
RX PubMed=8144675; DOI=10.2210/pdb1scu/pdb;
RA Wolodko W.T., Fraser M.E., James M.N.G., Bridger W.A.;
RT "The crystal structure of succinyl-CoA synthetase from Escherichia coli at
RT 2.5-A resolution.";
RL J. Biol. Chem. 269:10883-10890(1994).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUCC AND COENZYME A,
RP AND ACTIVE SITE.
RX PubMed=9917402; DOI=10.1006/jmbi.1998.2324;
RA Fraser M.E., James M.N., Bridger W.A., Wolodko W.T.;
RT "A detailed structural description of Escherichia coli succinyl-CoA
RT synthetase.";
RL J. Mol. Biol. 285:1633-1653(1999).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) IN COMPLEX WITH SUCC AND COENZYME A.
RX PubMed=10625475; DOI=10.1021/bi991696f;
RA Joyce M.A., Fraser M.E., James M.N., Bridger W.A., Wolodko W.T.;
RT "ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by
RT X-ray crystallography.";
RL Biochemistry 39:17-25(2000).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH SUCC AND COENZYME A,
RP ACTIVE SITE, AND MUTAGENESIS OF GLU-209.
RX PubMed=11781092; DOI=10.1021/bi011518y;
RA Fraser M.E., Joyce M.A., Ryan D.G., Wolodko W.T.;
RT "Two glutamate residues, Glu 208 alpha and Glu 197 beta, are crucial for
RT phosphorylation and dephosphorylation of the active-site histidine residue
RT in succinyl-CoA synthetase.";
RL Biochemistry 41:537-546(2002).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH SUCC AND COENZYME A.
RX PubMed=17642514; DOI=10.1107/s0907444907029319;
RA Hidber E., Brownie E.R., Hayakawa K., Fraser M.E.;
RT "Participation of Cys123alpha of Escherichia coli succinyl-CoA synthetase
RT in catalysis.";
RL Acta Crystallogr. D 63:876-884(2007).
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. Can use either
CC ATP or GTP, but prefers ATP. It can also function in the other
CC direction for anabolic purposes, and this may be particularly important
CC for providing succinyl-CoA during anaerobic growth when the oxidative
CC route from 2-oxoglutarate is severely repressed. {ECO:0000255|HAMAP-
CC Rule:MF_01988, ECO:0000269|PubMed:10353839}.
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_01988, ECO:0000269|PubMed:10353839};
CC -!- ACTIVITY REGULATION: Exhibits two interesting properties: 'substrate
CC synergism', in which the enzyme is most active for the catalysis of its
CC partial reactions only when all the substrate-binding sites are
CC occupied, and 'catalytic cooperativity' between alternating active
CC sites in the tetramer, whereby the interaction of substrates
CC (particularly ATP) at one site is needed to promote catalysis at the
CC other.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.25 mM for succinate {ECO:0000269|PubMed:10353839};
CC KM=4 uM for CoA {ECO:0000269|PubMed:10353839};
CC Note=kcat is 2684 min(-1) with ATP as substrate and 1471 min(-1) with
CC GTP as substrate. {ECO:0000269|PubMed:10353839};
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:10353839}.
CC -!- SUBUNIT: Heterotetramer of two alpha and two beta subunits.
CC {ECO:0000255|HAMAP-Rule:MF_01988, ECO:0000269|PubMed:8144675,
CC ECO:0000269|PubMed:9917402}.
CC -!- INTERACTION:
CC P0AGE9; P0A836: sucC; NbExp=4; IntAct=EBI-369078, EBI-369117;
CC -!- MISCELLANEOUS: Succinyl-CoA synthetase (SCS) of E.coli catalyzes its
CC reaction via three steps that involve phosphoryl enzyme and enzyme-
CC bound succinyl phosphate as intermediates.
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; J01619; AAA23900.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73823.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35395.1; -; Genomic_DNA.
DR EMBL; X15790; CAA33792.1; -; Genomic_DNA.
DR PIR; A90499; SYECSA.
DR RefSeq; NP_415257.1; NC_000913.3.
DR RefSeq; WP_000025458.1; NZ_STEB01000035.1.
DR PDB; 1CQI; X-ray; 3.30 A; A/D=2-287.
DR PDB; 1CQJ; X-ray; 2.90 A; A/D=2-287.
DR PDB; 1JKJ; X-ray; 2.35 A; A/D=2-289.
DR PDB; 1JLL; X-ray; 2.69 A; A/D=2-289.
DR PDB; 1SCU; X-ray; 2.50 A; A/D=2-289.
DR PDB; 2NU6; X-ray; 2.55 A; A/D=2-289.
DR PDB; 2NU7; X-ray; 2.20 A; A/D=2-289.
DR PDB; 2NU8; X-ray; 2.15 A; A/D=2-289.
DR PDB; 2NU9; X-ray; 2.90 A; A/D/F/H=2-289.
DR PDB; 2NUA; X-ray; 2.95 A; A/D=2-289.
DR PDB; 2SCU; X-ray; 2.30 A; A/D=2-289.
DR PDBsum; 1CQI; -.
DR PDBsum; 1CQJ; -.
DR PDBsum; 1JKJ; -.
DR PDBsum; 1JLL; -.
DR PDBsum; 1SCU; -.
DR PDBsum; 2NU6; -.
DR PDBsum; 2NU7; -.
DR PDBsum; 2NU8; -.
DR PDBsum; 2NU9; -.
DR PDBsum; 2NUA; -.
DR PDBsum; 2SCU; -.
DR AlphaFoldDB; P0AGE9; -.
DR SMR; P0AGE9; -.
DR BioGRID; 4259936; 56.
DR ComplexPortal; CPX-1092; Succinyl-CoA synthetase.
DR DIP; DIP-31851N; -.
DR IntAct; P0AGE9; 7.
DR STRING; 511145.b0729; -.
DR SWISS-2DPAGE; P0AGE9; -.
DR jPOST; P0AGE9; -.
DR PaxDb; P0AGE9; -.
DR PRIDE; P0AGE9; -.
DR EnsemblBacteria; AAC73823; AAC73823; b0729.
DR EnsemblBacteria; BAA35395; BAA35395; BAA35395.
DR GeneID; 67413769; -.
DR GeneID; 945314; -.
DR KEGG; ecj:JW0718; -.
DR KEGG; eco:b0729; -.
DR PATRIC; fig|1411691.4.peg.1544; -.
DR EchoBASE; EB0975; -.
DR eggNOG; COG0074; Bacteria.
DR HOGENOM; CLU_052104_0_0_6; -.
DR InParanoid; P0AGE9; -.
DR OMA; VIICITE; -.
DR PhylomeDB; P0AGE9; -.
DR BioCyc; EcoCyc:SUCCCOASYN-ALPHA; -.
DR BioCyc; MetaCyc:SUCCCOASYN-ALPHA; -.
DR BRENDA; 6.2.1.5; 2165.
DR UniPathway; UPA00223; UER00999.
DR EvolutionaryTrace; P0AGE9; -.
DR PRO; PR:P0AGE9; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; HDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0009361; C:succinate-CoA ligase complex (ADP-forming); IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0004775; F:succinate-CoA ligase (ADP-forming) activity; IBA:GO_Central.
DR GO; GO:0004776; F:succinate-CoA ligase (GDP-forming) activity; IBA:GO_Central.
DR GO; GO:0046777; P:protein autophosphorylation; IMP:EcoCyc.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IBA:GO_Central.
DR Gene3D; 3.40.50.261; -; 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; IPR005811; CoA_ligase.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR016102; Succinyl-CoA_synth-like.
DR Pfam; PF02629; CoA_binding; 1.
DR Pfam; PF00549; Ligase_CoA; 1.
DR PIRSF; PIRSF001553; SucCS_alpha; 1.
DR SMART; SM00881; CoA_binding; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF52210; SSF52210; 1.
DR TIGRFAMs; TIGR01019; sucCoAalpha; 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; Direct protein sequencing; Ligase; Nucleotide-binding;
KW Reference proteome; Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7783627,
FT ECO:0000269|PubMed:9298646, ECO:0000269|Ref.7"
FT CHAIN 2..289
FT /note="Succinate--CoA ligase [ADP-forming] subunit alpha"
FT /id="PRO_0000102791"
FT ACT_SITE 247
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988,
FT ECO:0000269|PubMed:11781092, ECO:0000269|PubMed:9917402"
FT BINDING 17..20
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988,
FT ECO:0000269|PubMed:10625475, ECO:0000269|PubMed:11781092,
FT ECO:0000269|PubMed:8144675, ECO:0000269|PubMed:9917402"
FT BINDING 43
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988,
FT ECO:0000269|PubMed:10625475, ECO:0000269|PubMed:11781092,
FT ECO:0000269|PubMed:8144675, ECO:0000269|PubMed:9917402"
FT BINDING 96..98
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988,
FT ECO:0000269|PubMed:10625475, ECO:0000269|PubMed:11781092,
FT ECO:0000269|PubMed:8144675, ECO:0000269|PubMed:9917402"
FT BINDING 159
FT /ligand="substrate"
FT /ligand_note="ligand shared with subunit beta"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01988"
FT MUTAGEN 209
FT /note="E->Q: Prevents phosphorylation of the enzyme
FT intermediate by succinyl-CoA and phosphate."
FT /evidence="ECO:0000269|PubMed:11781092"
FT STRAND 10..14
FT /evidence="ECO:0007829|PDB:2NU8"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 19..31
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:2NU7"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 57..64
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 91..95
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 102..115
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:2SCU"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:2NU8"
FT TURN 130..132
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:2NU7"
FT STRAND 145..153
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 155..167
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 180..183
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 188..196
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 203..213
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 214..225
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 230..235
FT /evidence="ECO:0007829|PDB:2NU8"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:2NUA"
FT HELIX 248..250
FT /evidence="ECO:0007829|PDB:2NUA"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:2NU7"
FT HELIX 259..268
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:2NU8"
FT HELIX 280..287
FT /evidence="ECO:0007829|PDB:2NU8"
SQ SEQUENCE 289 AA; 29777 MW; 8AC27AD828BC51B3 CRC64;
MSILIDKNTK VICQGFTGSQ GTFHSEQAIA YGTKMVGGVT PGKGGTTHLG LPVFNTVREA
VAATGATASV IYVPAPFCKD SILEAIDAGI KLIITITEGI PTLDMLTVKV KLDEAGVRMI
GPNCPGVITP GECKIGIQPG HIHKPGKVGI VSRSGTLTYE AVKQTTDYGF GQSTCVGIGG
DPIPGSNFID ILEMFEKDPQ TEAIVMIGEI GGSAEEEAAA YIKEHVTKPV VGYIAGVTAP
KGKRMGHAGA IIAGGKGTAD EKFAALEAAG VKTVRSLADI GEALKTVLK
