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A detailed description of the structure of Succinyl-COA synthetase from Escherichia coli

Source organism: Escherichia coli
Biochemical function: ligase activity
Biological process: tricarboxylic acid cycle
Cellular component: succinate-CoA ligase complex (ADP-forming)

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EC 6.2.1.5: Succinate--CoA ligase (ADP-forming)

Reaction catalysed:
ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
Systematic name:
Succinate:CoA ligase (ADP-forming)
Alternative Name(s):
  • A-SCS
  • A-STK (adenin nucleotide-linked succinate thiokinase)
  • STK
  • Succinate thiokinase
  • Succinic thiokinase
  • Succinyl coenzyme A synthetase
  • Succinyl coenzyme A synthetase (adenosine diphosphate-forming)
  • Succinyl-CoA synthetase
  • Succinyl-CoA synthetase (ADP-forming)

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00549
Domain description: CoA-ligase
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
  2. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of Pfam domain PF00549 (CoA-ligase) in Succinate--CoA ligase [ADP-forming] subunit alpha. Showing 1 copy in chain A.
The deposited structure of PDB entry 2scu contains 2 copies of Pfam domain PF00549 (CoA-ligase) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.

PF08442
Domain description: ATP-grasp domain
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of Pfam domain PF08442 (ATP-grasp domain) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.

PF02629
Domain description: CoA binding domain
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
The deposited structure of PDB entry 2scu contains 2 copies of Pfam domain PF02629 (CoA binding domain) in Succinate--CoA ligase [ADP-forming] subunit alpha. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR016102
Domain description: Succinyl-CoA synthetase-like
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
  2. Succinate--CoA ligase [ADP-forming] subunit beta
IPR005809
Domain description: Succinate--CoA ligase-like, beta subunit
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
IPR005810
Domain description: Succinyl-CoA ligase, alpha subunit
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
IPR005811
Domain description: ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
  2. Succinate--CoA ligase [ADP-forming] subunit beta
IPR003781
Domain description: CoA-binding
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
IPR017866
Domain description: Succinyl-CoA synthetase, beta subunit, conserved site
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
IPR013815
Domain description: ATP-grasp fold, subdomain 1
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
IPR011761
Domain description: ATP-grasp fold
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
IPR013650
Domain description: ATP-grasp fold, succinyl-CoA synthetase-type
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
IPR017440
Domain description: ATP-citrate lyase/succinyl-CoA ligase, active site
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
IPR033847
Domain description: ATP-citrate lyase/succinyl-CoA ligase, conserved site
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
IPR036291
Domain description: NAD(P)-binding domain superfamily
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha

Structure domains

CATH CATH domains
3.30.470.20
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: D-amino Acid Aminotransferase; Chain A, domain 1
Homology: ATP-grasp fold, B domain
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of CATH domain 3.30.470.20 (D-amino Acid Aminotransferase; Chain A, domain 1) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.
3.40.50.261
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Succinyl-CoA synthetase domains
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
  2. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of CATH domain 3.40.50.261 (Rossmann fold) in Succinate--CoA ligase [ADP-forming] subunit alpha. Showing 1 copy in chain A.
The deposited structure of PDB entry 2scu contains 2 copies of CATH domain 3.40.50.261 (Rossmann fold) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.
3.30.1490.20
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Dna Ligase; domain 1
Homology: ATP-grasp fold, A domain
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of CATH domain 3.30.1490.20 (Dna Ligase; domain 1) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.
3.40.50.720
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: NAD(P)-binding Rossmann-like Domain
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
The deposited structure of PDB entry 2scu contains 2 copies of CATH domain 3.40.50.720 (Rossmann fold) in Succinate--CoA ligase [ADP-forming] subunit alpha. Showing 1 copy in chain A.
SCOP SCOP annotations
52211
Class: Alpha and beta proteins (a/b)
Fold: Flavodoxin-like
Superfamily: Succinyl-CoA synthetase domains
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
  2. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of SCOP domain 52211 (Succinyl-CoA synthetase domains) in Succinate--CoA ligase [ADP-forming] subunit alpha. Showing 1 copy in chain A.
The deposited structure of PDB entry 2scu contains 2 copies of SCOP domain 52211 (Succinyl-CoA synthetase domains) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.
56081
Class: Alpha and beta proteins (a+b)
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit beta
The deposited structure of PDB entry 2scu contains 2 copies of SCOP domain 56081 (Succinyl-CoA synthetase, beta-chain, N-terminal domain) in Succinate--CoA ligase [ADP-forming] subunit beta. Showing 1 copy in chain B.
51900
Class: Alpha and beta proteins (a/b)
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Occurring in:
  1. Succinate--CoA ligase [ADP-forming] subunit alpha
The deposited structure of PDB entry 2scu contains 2 copies of SCOP domain 51900 (CoA-binding domain) in Succinate--CoA ligase [ADP-forming] subunit alpha. Showing 1 copy in chain A.

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