1CQI

Crystal Structure of the Complex of ADP and MG2+ with Dephosphorylated E. Coli Succinyl-CoA Synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.

(2000) Biochemistry 39: 17-25

  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Related Citations: 
    • The Crystal Structure of Succinyl-Coa Synthetase from Escherichia Coli at 2.5A Resolution
      Wolodko, W.T.,Fraser, M.E.,James, M.N.G.,Bridger, W.A.
      (1994) J.Biol.Chem. 269: 10883
    • Crystallization of Succinyl-Coa Synthetase from Escherichia Coli
      Wolodko, W.T.,James, M.N.G.,Bridger, W.A.
      (1984) J.Biol.Chem. 259: 5316
    • A Detailed Structural Description of Escherichia Coli Succinyl-Coa Synthetase
      Fraser, M.E.,James, M.N.G.,Bridger, W.A.,Wolodko, W.T.
      (1999) J.Mol.Biol. 285: 1633


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SUCCINYL-COA SYNTHETASE ALPHA CHAIN)
A, D
286Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sucD
EC: 6.2.1.5
Find proteins for P0AGE9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGE9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SUCCINYL-COA SYNTHETASE BETA CHAIN)
B, E
385Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sucC
EC: 6.2.1.5
Find proteins for P0A836 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A836
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
B, E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, D
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.860α = 90.00
b = 99.860β = 90.00
c = 407.150γ = 90.00
Software Package:
Software NamePurpose
KBAPLYdata scaling
SCALKB2data scaling
CNSrefinement
BIOMOLmodel building
WEISdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-07
    Type: Initial release
  • Version 1.1: 2007-10-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description