3UFX

Thermus aquaticus succinyl-CoA synthetase in complex with GDP-Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus.

Joyce, M.A.Hayakawa, K.Wolodko, W.T.Fraser, M.E.

(2012) Acta Crystallogr.,Sect.D 68: 751-762

  • DOI: 10.1107/S0907444912010852

  • PubMed Abstract: 
  • Succinyl-CoA synthetase (SCS) from Thermus aquaticus was characterized biochemically via measurements of the activity of the enzyme and determination of its quaternary structure as well as its stability and refolding properties. The enzyme is most ac ...

    Succinyl-CoA synthetase (SCS) from Thermus aquaticus was characterized biochemically via measurements of the activity of the enzyme and determination of its quaternary structure as well as its stability and refolding properties. The enzyme is most active between pH 8.0 and 8.4 and its activity increases with temperature to about 339 K. Gel-filtration chromatography and sedimentation equilibrium under native conditions demonstrated that the enzyme is a heterotetramer of two α-subunits and two β-subunits. The activity assays showed that the enzyme uses either ADP/ATP or GDP/GTP, but prefers GDP/GTP. This contrasts with Escherichia coli SCS, which uses GDP/GTP but prefers ADP/ATP. To understand the nucleotide preference, T. aquaticus SCS was crystallized in the presence of GDP, leading to the determination of the structure in complex with GDP-Mn(2+). A water molecule and Pro20β in T. aquaticus take the place of Gln20β in pig GTP-specific SCS, interacting well with the guanine base and other residues of the nucleotide-binding site. This leads to the preference for GDP/GTP, but does not hinder the binding of ADP/ATP.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
succinyl-CoA synthetase alpha subunit
A, D, F, H
296Thermus thermophilusMutation(s): 0 
Gene Names: sucD (scsA)
EC: 6.2.1.4
Find proteins for P09143 (Thermus thermophilus)
Go to UniProtKB:  P09143
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA synthetase beta subunit
B, E, G, I
397Thermus thermophilusMutation(s): 0 
Gene Names: sucC (scsB)
EC: 6.2.1.4
Find proteins for P25126 (Thermus thermophilus)
Go to UniProtKB:  P25126
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, E, G, I
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
B, E, G, I
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 261.700α = 90.00
b = 126.800β = 112.76
c = 110.600γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-01 
  • Released Date: 2012-06-27 
  • Deposition Author(s): Fraser, M.E.

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description