1JUY

REFINED CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH HYDANTOCIDIN 5'-PHOSPHATE GDP, HPO4(2-), MG2+, AND HADACIDIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin.

Poland, B.W.Lee, S.F.Subramanian, M.V.Siehl, D.L.Anderson, R.J.Fromm, H.J.Honzatko, R.B.

(1996) Biochemistry 35: 15753-15759

  • DOI: 10.1021/bi961758r

  • PubMed Abstract: 
  • A crystal structure of adenylosuccinate synthetase from Escherichia coli, complexed with 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin at 100 K, has been refined to an Rfactor of 0.195 against data to 2.6 A resolution. Bond lengths and angles devi ...

    A crystal structure of adenylosuccinate synthetase from Escherichia coli, complexed with 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin at 100 K, has been refined to an Rfactor of 0.195 against data to 2.6 A resolution. Bond lengths and angles deviate from expected values by 0.012 A and 1.86 degrees, respectively. Lys 16 and backbone amides 15-17 and 42 interact with the phosphates of GDP, while Ser 414, Asp 333, and backbone amides 331 and 416 interact with the base. Mg2+ is octahedrally coordinated. Oxygen atoms from GDP, phosphate, and hadacidin define the equatorial plane of coordination of the Mg2+, while backbone carbonyl 40 and the side chain of Asp 13 are the apical ligands. HPO4(2-) hydrogen bonds with Lys 16, His 41, backbone amides 13, 40, and 224, and the base moiety of the hydantocidin inhibitor. The carboxylate of hadacidin interacts with Arg 303 and Thr 301; its N-formyl group coordinates to Mg2+, and its hydroxyl group hydrogen bonds with Asp 13. The 5'-phosphate of the hydantocidin inhibitor interacts with Asn 38, Thr 129, and Thr 239 but is approximately 3.5 A from Arg 143 (related by molecular 2-fold symmetry). The base moiety of hydantocidin 5'-phosphate hydrogen bonds to Gln 224 and participates in a hydrogen-bonded network that includes the phosphate molecule, several water molecules, and Asp 13. Hydantocidin 5'-phosphate, GDP, HPO4(2-), and Mg2+ may represent a set of synergistic inhibitors even more effective than the combination of IMP, GDP, NO3-, and Mg2+.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Iowa State University, Ames 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 5 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
PI
Query on PI

Download SDF File 
Download CCD File 
A
HYDROGENPHOSPHATE ION
H O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-L
 Ligand Interaction
H5P
Query on H5P

Download SDF File 
Download CCD File 
A
HYDANTOCIDIN-5'-PHOSPHATE
C7 H11 N2 O9 P
HVXIMXHBUJADCC-GTBMBKLPSA-N
 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H5PKi: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.400α = 90.00
b = 80.400β = 90.00
c = 158.410γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
XENGENdata scaling
X-PLORrefinement
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-06-24
    Type: Initial release
  • Version 1.1: 2008-03-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other