PDBsum entry: 1cqi

Ligase

PDB id: 1cqi

Contents

Protein chains

286 a.a. *

385 a.a. *

Ligands

PO4 ×2

COA ×2

ADP ×2

Metals

_MG ×2

* Residue conservation analysis

PDB id:

1cqi

Name:

Ligase

Title:

Crystal structure of the complex of adp and mg2+ with dephosphorylated e. Coli succinyl-coa synthetase

Structure:

Protein (succinyl-coa synthetase alpha chain). Chain: a, d. Fragment: alpha subunit. Synonym: scs-alpha. Engineered: yes. Protein (succinyl-coa synthetase beta chain). Chain: b, e. Fragment: beta subunit. Synonym: scs-beta.

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

3.30Å R-factor: 0.191 R-free: 0.247

Authors:

M.A.Joyce,M.E.Fraser,M.N.G.James,W.A.Bridger,W.T.Wolodko

Key ref:

M.A.Joyce et al. (2000). ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography. Biochemistry, 39, 17-25. PubMed id: 10625475 DOI: 10.1021/bi991696f

Date:

06-Aug-99 Release date: 07-Jan-00

Protein chains

P0AGE9  (SUCD_ECOLI) -  Succinyl-CoA ligase [ADP-forming] subunit alpha

Seq: 289 a.a.

Struc: 286 a.a.

Protein chains

P0A836  (SUCC_ECOLI) -  Succinyl-CoA ligase [ADP-forming] subunit beta

Seq: 388 a.a.

Struc: 385 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, D, E: E.C.6.2.1.5 - Succinate--CoA ligase (ADP-forming).
• Reaction: ATP + succinate + CoA = ADP + phosphate + succinyl-CoA

ATP + succinate + CoA = ADP + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) + succinyl-CoA (Bound ligand (Het Group name = COA) matches with 87.00% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (8 terms)

reference

DOI no: 10.1021/bi991696f

Biochemistry 39:17-25 (2000)

PubMed id: 10625475

ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.

M.A.Joyce, M.E.Fraser, M.N.James, W.A.Bridger, W.T.Wolodko.

ABSTRACT

Succinyl-CoA synthetase (SCS) catalyzes the following reversible reaction via a phosphorylated histidine intermediate (His 246alpha): succinyl-CoA + P(i) + NDP <--> succinate + CoA + NTP (N denotes adenosine or guanosine). To determine the structure of the enzyme with nucleotide bound, crystals of phosphorylated Escherichia coli SCS were soaked in successive experiments adopting progressive strategies. In the first experiment, 1 mM ADP (>15 x K(d)) was added; Mg(2+) ions were omitted to preclude the formation of an insoluble precipitate with the phosphate and ammonium ions. X-ray crystallography revealed that the enzyme was dephosphorylated, but the nucleotide did not remain bound to the enzyme (R(working) = 17.2%, R(free) = 22.8% for data to 2.9 A resolution). Catalysis requires Mg(2+) ions; hence, the "true" nucleotide substrate is probably an ADP-Mg(2+) complex. In the successful experiment, the phosphate buffer was exchanged with MOPS, the concentration of sulfate ions was lowered, and the concentrations of ADP and Mg(2+) ions were increased to 10.5 and 50 mM, respectively. X-ray diffraction data revealed an ADP-Mg(2+) complex bound in the ATP-grasp fold of the N-terminal domain of each beta-subunit (R(working) = 19.1%, R(free) = 24.7% for data to 3.3 A resolution). We describe the specific interactions of the nucleotide-Mg(2+) complex with SCS, compare these results with those for other proteins containing the ATP-grasp fold, and present a hypothetical model of the histidine-containing loop in the "down" position where it can interact with the nucleotide approximately 35 A from where His 246alpha is seen in both phosphorylated and dephosphorylated SCS.