1KSZ

ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRYSTALLINE ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI, DATA COLLECTED AT 298K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli.

Poland, B.W.Bruns, C.Fromm, H.J.Honzatko, R.B.

(1997) J.Biol.Chem. 272: 15200-15205

  • Primary Citation of Related Structures:  1NHT

  • PubMed Abstract: 
  • Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with Mg2+, 6-thiophosphoryl-IMP, GDP, and hadacidin at 298 and 100 K have been refined to R-factors of 0.171 and 0.206 against data to 2.8 and 2.5 A resolution, respect ...

    Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with Mg2+, 6-thiophosphoryl-IMP, GDP, and hadacidin at 298 and 100 K have been refined to R-factors of 0.171 and 0.206 against data to 2.8 and 2.5 A resolution, respectively. Interactions of GDP, Mg2+ and hadacidin are similar to those observed for the same ligands in the complex of IMP, GDP, NO3-, Mg2+ and hadacidin (Poland, B. W., Fromm, H. J. & Honzatko, R. B. (1996). J. Mol. Biol. 264, 1013-1027). Although crystals were grown from solutions containing 6-mercapto-IMP and GTP, the electron density at the active site is consistent with 6-thiophosphoryl-IMP and GDP. Asp-13 and Gln-224 probably work in concert to stabilize the 6-thioanion of 6-mercapto-IMP, which in turn is the nucleophile in the displacement of GDP from the gamma-phosphate of GTP. Once formed, 6-thiophosphoryl-IMP is stable in the active site of the enzyme under the conditions of the structural investigation. The direct observation of 6-thiophosphoryl-IMP in the active site is consistent with the putative generation of 6-phosphoryl-IMP along the reaction pathway of the synthetase.


    Related Citations: 
    • Crystal Structure of Adenylosuccinate Synthetase from Escherichia Coli. Evidence for Convergent Evolution of GTP-Binding Domains
      Poland, B.W.,Silva, M.M.,Serra, M.A.,Cho, Y.,Kim, K.H.,Harris, E.M.,Honzatko, R.B.
      (1993) J.Biol.Chem. 268: 25334
    • Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from Escherichia Coli
      Silva, M.M.,Poland, B.W.,Hoffman, C.R.,Fromm, H.J.,Honzatko, R.B.
      (1995) J.Mol.Biol. 254: 431


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLOSUCCINATE SYNTHETASE
A
431Escherichia coli (strain K12)Gene Names: purA (adeK)
EC: 6.3.4.4
Find proteins for P0A7D4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7D4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PGS
Query on PGS

Download SDF File 
Download CCD File 
A
2-DEAZO-6-THIOPHOSPHATE GUANOSINE-5'-MONOPHOSPHATE
C10 H15 N4 O10 P2 S
NYBPOGVUIOPXHI-KQYNXXCUSA-O
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HDA
Query on HDA

Download SDF File 
Download CCD File 
A
HADACIDIN
C3 H5 N O4
URJHVPKUWOUENU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.630α = 90.00
b = 81.630β = 90.00
c = 159.220γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other