1GIM

CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH GDP, IMP, HADACIDIN, NO3-, AND MG2+. DATA COLLECTED AT 100K (PH 6.5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+.

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

(1996) J Mol Biol 264: 1013-1027

  • DOI: 10.1006/jmbi.1996.0693
  • Primary Citation of Related Structures:  
    1GIN, 1GIM

  • PubMed Abstract: 
  • Crystal structures of adenylosuccinate synthetase from Esherichia coli complexed with Mg2+, IMP, GDP, NO3- and hadacidin at 298 and 100 K have been refined to R-factors of 0.188 and 0.206 against data to 2.8 A and 2.5 A resolution, respectively. Conformational changes of up to 9 A relative to the unligated enzyme occur in loops that bind to Mg2+, GDP, IMP and hadacidin ...

    Crystal structures of adenylosuccinate synthetase from Esherichia coli complexed with Mg2+, IMP, GDP, NO3- and hadacidin at 298 and 100 K have been refined to R-factors of 0.188 and 0.206 against data to 2.8 A and 2.5 A resolution, respectively. Conformational changes of up to 9 A relative to the unligated enzyme occur in loops that bind to Mg2+, GDP, IMP and hadacidin. Mg2+ binds directly to GDP, NO3-, hadacidin and the protein, but is only five-coordinated. Asp13, which approaches, but does not occupy the sixth coordination site of Mg2+, hydrogen bonds to N1 of IMP. The nitrogen atom of NO3- is approximately 2.7 A from O6 of IMP, reflecting a strong electrostatic interaction between the electron-deficient nitrogen atom and the electron-rich O6. The spatial relationships between GDP, NO3- and Mg2+ suggest an interaction between the beta,gamma-bridging oxygen atom of GTP and Mg2+ in the enzyme-substrate complex. His41 hydrogen bonds to the beta-phosphate group of GDP and approaches bound NO3-. The aldehyde group of hadacidin coordinates to the Mg2+, while its carboxyl group interacts with backbone amide groups 299 to 303 and the side-chain of Arg303. The 5'-phosphate group of IMP interacts with Asn38, Thr129, Thr239 and Arg143 (from a monomer related by 2-fold symmetry). A mechanism is proposed for the two-step reaction governed by the synthetase, in which His41 and Asp13 are essential catalytic side-chains.


    Related Citations: 
    • Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from E.Coli
      Silva, M.M., Poland, B.W., Hoffman, C.R., Fromm, H.J., Honzatko, R.B.
      (1995) J Mol Biol 254: 431
    • Crystal Structure of Adenylosuccinate Synthetase from E.Coli
      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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADENYLOSUCCINATE SYNTHETASEA431Escherichia coliMutation(s): 0 
EC: 6.3.4.4
UniProt
Find proteins for P0A7D4 (Escherichia coli (strain K12))
Explore P0A7D4 
Go to UniProtKB:  P0A7D4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
IMP (Subject of Investigation/LOI)
Query on IMP

Download Ideal Coordinates CCD File 
E [auth A]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
HDA
Query on HDA

Download Ideal Coordinates CCD File 
D [auth A]HADACIDIN
C3 H5 N O4
URJHVPKUWOUENU-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.82α = 90
b = 80.82β = 90
c = 159.03γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2018-03-07
    Changes: Data collection