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Protein

Succinyl-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

During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. 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. The alpha-subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact.

Catalytic activityi

ATP + succinate + CoA = ADP + phosphate + succinyl-CoA.

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.

Pathwayi: tricarboxylic acid cycle

This protein is involved in step 1 of the subpathway that synthesizes succinate from succinyl-CoA (ligase route).
Proteins known to be involved in this subpathway in this organism are:
  1. Succinyl-CoA ligase [ADP-forming] subunit beta (sucC), Succinyl-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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei247 – 2471Tele-phosphohistidine intermediate

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:SUCCCOASYN-ALPHA.
ECOL316407:JW0718-MONOMER.
MetaCyc:SUCCCOASYN-ALPHA.
BRENDAi6.2.1.5. 2165.
UniPathwayiUPA00223; UER00999.

Names & Taxonomyi

Protein namesi
Recommended name:
Succinyl-CoA ligase [ADP-forming] subunit alpha (EC:6.2.1.5)
Alternative name(s):
Succinyl-CoA synthetase subunit alpha
Short name:
SCS-alpha
Gene namesi
Name:sucD
Ordered Locus Names:b0729, JW0718
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved3 Publications
Chaini2 – 289288Succinyl-CoA ligase [ADP-forming] subunit alphaPRO_0000102791Add
BLAST

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP0AGE9.
PaxDbiP0AGE9.
PRIDEiP0AGE9.

2D gel databases

SWISS-2DPAGEP0AGE9.

Interactioni

Subunit structurei

Heterotetramer of two alpha and two beta subunits.

Binary interactionsi

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

Protein-protein interaction databases

BioGridi4259936. 23 interactions.
DIPiDIP-31851N.
IntActiP0AGE9. 7 interactions.
MINTiMINT-1219451.
STRINGi511145.b0729.

Structurei

Secondary structure

1
289
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 145Combined sources
Turni15 – 173Combined sources
Helixi19 – 3113Combined sources
Beta strandi34 – 396Combined sources
Beta strandi46 – 483Combined sources
Beta strandi51 – 566Combined sources
Helixi57 – 648Combined sources
Beta strandi68 – 714Combined sources
Helixi75 – 773Combined sources
Helixi78 – 8710Combined sources
Beta strandi91 – 955Combined sources
Helixi102 – 11514Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi122 – 1243Combined sources
Beta strandi126 – 1294Combined sources
Turni130 – 1323Combined sources
Beta strandi133 – 1386Combined sources
Helixi140 – 1423Combined sources
Beta strandi145 – 1539Combined sources
Helixi155 – 16713Combined sources
Beta strandi172 – 1776Combined sources
Beta strandi180 – 1834Combined sources
Helixi188 – 1969Combined sources
Beta strandi203 – 21311Combined sources
Helixi214 – 22512Combined sources
Beta strandi230 – 2356Combined sources
Beta strandi241 – 2433Combined sources
Helixi248 – 2503Combined sources
Helixi253 – 2553Combined sources
Helixi259 – 26810Combined sources
Helixi277 – 2793Combined sources
Helixi280 – 2878Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-288.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AGE9.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CH8. Bacteria.
COG0074. LUCA.
HOGENOMiHOG000239685.
InParanoidiP0AGE9.
KOiK01902.
OMAiFEQDPQT.
OrthoDBiEOG644ZT0.
PhylomeDBiP0AGE9.

Family and domain databases

Gene3Di3.40.50.261. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR017440. Cit_synth/succinyl-CoA_lig_AS.
IPR003781. CoA-bd.
IPR005810. CoA_lig_alpha.
IPR005811. CoA_ligase.
IPR016040. NAD(P)-bd_dom.
IPR016102. Succinyl-CoA_synth-like.
[Graphical view]
PfamiPF02629. CoA_binding. 1 hit.
PF00549. Ligase_CoA. 1 hit.
[Graphical view]
PIRSFiPIRSF001553. SucCS_alpha. 1 hit.
PRINTSiPR01798. SCOASYNTHASE.
SMARTiSM00881. CoA_binding. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF52210. SSF52210. 1 hit.
TIGRFAMsiTIGR01019. sucCoAalpha. 1 hit.
PROSITEiPS01216. SUCCINYL_COA_LIG_1. 1 hit.
PS00399. SUCCINYL_COA_LIG_2. 1 hit.
[Graphical view]

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.
PATRICi32116653. VBIEscCol129921_0759.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-288.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259936. 23 interactions.
DIPiDIP-31851N.
IntActiP0AGE9. 7 interactions.
MINTiMINT-1219451.
STRINGi511145.b0729.

2D gel databases

SWISS-2DPAGEP0AGE9.

Proteomic databases

EPDiP0AGE9.
PaxDbiP0AGE9.
PRIDEiP0AGE9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73823; AAC73823; b0729.
BAA35395; BAA35395; BAA35395.
GeneIDi945314.
KEGGiecj:JW0718.
eco:b0729.
PATRICi32116653. VBIEscCol129921_0759.

Organism-specific databases

EchoBASEiEB0975.
EcoGeneiEG10982. sucD.

Phylogenomic databases

eggNOGiENOG4105CH8. Bacteria.
COG0074. LUCA.
HOGENOMiHOG000239685.
InParanoidiP0AGE9.
KOiK01902.
OMAiFEQDPQT.
OrthoDBiEOG644ZT0.
PhylomeDBiP0AGE9.

Enzyme and pathway databases

UniPathwayiUPA00223; UER00999.
BioCyciEcoCyc:SUCCCOASYN-ALPHA.
ECOL316407:JW0718-MONOMER.
MetaCyc:SUCCCOASYN-ALPHA.
BRENDAi6.2.1.5. 2165.

Miscellaneous databases

EvolutionaryTraceiP0AGE9.
PROiP0AGE9.

Family and domain databases

Gene3Di3.40.50.261. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR017440. Cit_synth/succinyl-CoA_lig_AS.
IPR003781. CoA-bd.
IPR005810. CoA_lig_alpha.
IPR005811. CoA_ligase.
IPR016040. NAD(P)-bd_dom.
IPR016102. Succinyl-CoA_synth-like.
[Graphical view]
PfamiPF02629. CoA_binding. 1 hit.
PF00549. Ligase_CoA. 1 hit.
[Graphical view]
PIRSFiPIRSF001553. SucCS_alpha. 1 hit.
PRINTSiPR01798. SCOASYNTHASE.
SMARTiSM00881. CoA_binding. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF52210. SSF52210. 1 hit.
TIGRFAMsiTIGR01019. sucCoAalpha. 1 hit.
PROSITEiPS01216. SUCCINYL_COA_LIG_1. 1 hit.
PS00399. SUCCINYL_COA_LIG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Primary structure of the succinyl-CoA synthetase of Escherichia coli."
    Buck D., Spencer M.E., Guest J.R.
    Biochemistry 24:6245-6252(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon."
    Buck D., Guest J.R.
    Biochem. J. 260:737-747(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 173-289.
  6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-20.
    Strain: K12 / EMG2.
  7. Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F.
    Submitted (FEB-1996) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 2-12.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  8. "Identification of phosphoproteins in Escherichia coli."
    Freestone P., Grant S., Toth I., Norris V.
    Mol. Microbiol. 15:573-580(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION, PROTEIN SEQUENCE OF 2-11.
  9. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  10. "The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-A resolution."
    Wolodko W.T., Fraser M.E., James M.N.G., Bridger W.A.
    J. Biol. Chem. 269:10883-10890(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  11. "A detailed structural description of Escherichia coli succinyl-CoA synthetase."
    Fraser M.E., James M.N., Bridger W.A., Wolodko W.T.
    J. Mol. Biol. 285:1633-1653(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
  12. "ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by X-ray crystallography."
    Joyce M.A., Fraser M.E., James M.N., Bridger W.A., Wolodko W.T.
    Biochemistry 39:17-25(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS).

Entry informationi

Entry nameiSUCD_ECOLI
AccessioniPrimary (citable) accession number: P0AGE9
Secondary accession number(s): P07459
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: March 16, 2016
This is version 92 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.
The succinyl-CoA synthetases of eukaryotes and Gram-positive bacteria differ from the Gram-negative enzymes in containing single alpha-beta dimers.

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.