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Protein

Succinate--CoA ligase [ADP-forming] subunit alpha

Gene

sucD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit. Can use either ATP or GTP, but prefers ATP. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed.UniRule annotation1 Publication

Miscellaneous

Succinyl-CoA synthetase (SCS) of E.coli catalyzes its reaction via three steps that involve phosphoryl enzyme and enzyme-bound succinyl phosphate as intermediates.

Catalytic activityi

ATP + succinate + CoA = ADP + phosphate + succinyl-CoA.UniRule annotation1 Publication

Enzyme regulationi

Exhibits two interesting properties: "substrate synergism", in which the enzyme is most active for the catalysis of its partial reactions only when all the substrate-binding sites are occupied, and "catalytic cooperativity" between alternating active sites in the tetramer, whereby the interaction of substrates (particularly ATP) at one site is needed to promote catalysis at the other.

Kineticsi

kcat is 2684 min(-1) with ATP as substrate and 1471 min(-1) with GTP as substrate.1 Publication
  1. KM=0.25 mM for succinate1 Publication
  2. KM=4 µM for CoA1 Publication

    Pathwayi: tricarboxylic acid cycle

    This protein is involved in step 1 of the subpathway that synthesizes succinate from succinyl-CoA (ligase route).UniRule annotation1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Succinate--CoA ligase [ADP-forming] subunit beta (sucC), Succinate--CoA ligase [ADP-forming] subunit alpha (sucD)
    This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes succinate from succinyl-CoA (ligase route), the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei43Coenzyme AUniRule annotation4 Publications1
    Binding sitei159Substrate; shared with subunit betaUniRule annotation1
    Active sitei247Tele-phosphohistidine intermediateUniRule annotation2 Publications1

    GO - Molecular functioni

    GO - Biological processi

    • protein autophosphorylation Source: EcoCyc
    • tricarboxylic acid cycle Source: UniProtKB-UniPathway

    Keywordsi

    Molecular functionLigase
    Biological processTricarboxylic acid cycle
    LigandNucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:SUCCCOASYN-ALPHA.
    MetaCyc:SUCCCOASYN-ALPHA.
    BRENDAi6.2.1.5. 2165.
    UniPathwayiUPA00223; UER00999.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Succinate--CoA ligase [ADP-forming] subunit alphaUniRule annotation (EC:6.2.1.5UniRule annotation1 Publication)
    Alternative name(s):
    Succinyl-CoA synthetase subunit alphaUniRule annotation
    Short name:
    SCS-alphaUniRule annotation
    Gene namesi
    Name:sucDUniRule annotation
    Ordered Locus Names:b0729, JW0718
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10982. sucD.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: UniProtKB
    • cytosol Source: EcoCyc
    • succinate-CoA ligase complex (ADP-forming) Source: EcoCyc

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi209E → Q: Prevents phosphorylation of the enzyme intermediate by succinyl-CoA and phosphate. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved3 Publications
    ChainiPRO_00001027912 – 289Succinate--CoA ligase [ADP-forming] subunit alphaAdd BLAST288

    Proteomic databases

    PaxDbiP0AGE9.
    PRIDEiP0AGE9.

    2D gel databases

    SWISS-2DPAGEiP0AGE9.

    Interactioni

    Subunit structurei

    Heterotetramer of two alpha and two beta subunits.UniRule annotation2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    sucCP0A8363EBI-369078,EBI-369117

    Protein-protein interaction databases

    BioGridi4259936. 23 interactors.
    DIPiDIP-31851N.
    IntActiP0AGE9. 7 interactors.
    MINTiMINT-1219451.
    STRINGi316385.ECDH10B_0795.

    Structurei

    Secondary structure

    1289
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi10 – 14Combined sources5
    Turni15 – 17Combined sources3
    Helixi19 – 31Combined sources13
    Beta strandi34 – 39Combined sources6
    Beta strandi46 – 48Combined sources3
    Beta strandi51 – 56Combined sources6
    Helixi57 – 64Combined sources8
    Beta strandi68 – 71Combined sources4
    Helixi75 – 77Combined sources3
    Helixi78 – 87Combined sources10
    Beta strandi91 – 95Combined sources5
    Helixi102 – 115Combined sources14
    Beta strandi118 – 120Combined sources3
    Beta strandi122 – 124Combined sources3
    Beta strandi126 – 129Combined sources4
    Turni130 – 132Combined sources3
    Beta strandi133 – 138Combined sources6
    Helixi140 – 142Combined sources3
    Beta strandi145 – 153Combined sources9
    Helixi155 – 167Combined sources13
    Beta strandi172 – 177Combined sources6
    Beta strandi180 – 183Combined sources4
    Helixi188 – 196Combined sources9
    Beta strandi203 – 213Combined sources11
    Helixi214 – 225Combined sources12
    Beta strandi230 – 235Combined sources6
    Beta strandi241 – 243Combined sources3
    Helixi248 – 250Combined sources3
    Helixi253 – 255Combined sources3
    Helixi259 – 268Combined sources10
    Helixi277 – 279Combined sources3
    Helixi280 – 287Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1CQIX-ray3.30A/D2-287[»]
    1CQJX-ray2.90A/D2-287[»]
    1JKJX-ray2.35A/D2-289[»]
    1JLLX-ray2.69A/D2-289[»]
    1SCUX-ray2.50A/D2-289[»]
    2NU6X-ray2.55A/D2-289[»]
    2NU7X-ray2.20A/D2-289[»]
    2NU8X-ray2.15A/D2-289[»]
    2NU9X-ray2.90A/D/F/H2-289[»]
    2NUAX-ray2.95A/D2-289[»]
    2SCUX-ray2.30A/D2-289[»]
    ProteinModelPortaliP0AGE9.
    SMRiP0AGE9.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AGE9.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni17 – 20Coenzyme A bindingUniRule annotation4 Publications4
    Regioni96 – 98Coenzyme A bindingUniRule annotation4 Publications3

    Sequence similaritiesi

    Belongs to the succinate/malate CoA ligase alpha subunit family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CH8. Bacteria.
    COG0074. LUCA.
    HOGENOMiHOG000239685.
    InParanoidiP0AGE9.
    KOiK01902.
    PhylomeDBiP0AGE9.

    Family and domain databases

    Gene3Di3.40.50.261. 1 hit.
    HAMAPiMF_01988. Succ_CoA_alpha. 1 hit.
    InterProiView protein in InterPro
    IPR017440. Cit_synth/succinyl-CoA_lig_AS.
    IPR033847. Citrt_syn/SCS-alpha_CS.
    IPR003781. CoA-bd.
    IPR005810. CoA_lig_alpha.
    IPR005811. CoA_ligase.
    IPR016040. NAD(P)-bd_dom.
    IPR016102. Succinyl-CoA_synth-like.
    PfamiView protein in Pfam
    PF02629. CoA_binding. 1 hit.
    PF00549. Ligase_CoA. 1 hit.
    PIRSFiPIRSF001553. SucCS_alpha. 1 hit.
    SMARTiView protein in SMART
    SM00881. CoA_binding. 1 hit.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    SSF52210. SSF52210. 1 hit.
    TIGRFAMsiTIGR01019. sucCoAalpha. 1 hit.
    PROSITEiView protein in PROSITE
    PS01216. SUCCINYL_COA_LIG_1. 1 hit.
    PS00399. SUCCINYL_COA_LIG_2. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0AGE9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSILIDKNTK VICQGFTGSQ GTFHSEQAIA YGTKMVGGVT PGKGGTTHLG
    60 70 80 90 100
    LPVFNTVREA VAATGATASV IYVPAPFCKD SILEAIDAGI KLIITITEGI
    110 120 130 140 150
    PTLDMLTVKV KLDEAGVRMI GPNCPGVITP GECKIGIQPG HIHKPGKVGI
    160 170 180 190 200
    VSRSGTLTYE AVKQTTDYGF GQSTCVGIGG DPIPGSNFID ILEMFEKDPQ
    210 220 230 240 250
    TEAIVMIGEI GGSAEEEAAA YIKEHVTKPV VGYIAGVTAP KGKRMGHAGA
    260 270 280
    IIAGGKGTAD EKFAALEAAG VKTVRSLADI GEALKTVLK
    Length:289
    Mass (Da):29,777
    Last modified:January 23, 2007 - v2
    Checksum:i8AC27AD828BC51B3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J01619 Genomic DNA. Translation: AAA23900.1.
    U00096 Genomic DNA. Translation: AAC73823.1.
    AP009048 Genomic DNA. Translation: BAA35395.1.
    X15790 Genomic DNA. Translation: CAA33792.1.
    PIRiA90499. SYECSA.
    RefSeqiNP_415257.1. NC_000913.3.
    WP_000025458.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73823; AAC73823; b0729.
    BAA35395; BAA35395; BAA35395.
    GeneIDi945314.
    KEGGiecj:JW0718.
    eco:b0729.
    PATRICifig|1411691.4.peg.1544.

    Similar proteinsi

    Entry informationi

    Entry nameiSUCD_ECOLI
    AccessioniPrimary (citable) accession number: P0AGE9
    Secondary accession number(s): P07459
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1988
    Last sequence update: January 23, 2007
    Last modified: August 30, 2017
    This is version 103 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families