PDBsum entry 1son

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protein ligands links
Ligase PDB id
Jmol PyMol
Protein chain
431 a.a. *
Waters ×93
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Adenylosuccinate synthetase in complex with the natural feed inhibitor amp
Structure: Adenylosuccinate synthetase. Chain: a. Ec:
Source: Escherichia coli. Organism_taxid: 562. Strain: pur a strain h1238
Biol. unit: Dimer (from PDB file)
2.55Å     R-factor:   0.187    
Authors: S.W.Cowan-Jacob
Key ref: R.Fonné-Pfister et al. (1996). The mode of action and the structure of a herbicide in complex with its target: binding of activated hydantocidin to the feedback regulation site of adenylosuccinate synthetase. Proc Natl Acad Sci U S A, 93, 9431-9436. PubMed id: 8790347
07-May-96     Release date:   04-Sep-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase
432 a.a.
431 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Adenylosuccinate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

AMP and GMP Biosynthesis
      Reaction: GTP + IMP + L-aspartate = GDP + phosphate + N6-(1,2-dicarboxyethyl)- AMP
Bound ligand (Het Group name = AMP)
matches with 91.67% similarity
+ L-aspartate
+ phosphate
+ N(6)-(1,2-dicarboxyethyl)- AMP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     'de novo' AMP biosynthetic process   6 terms 
  Biochemical function     nucleotide binding     6 terms  


Proc Natl Acad Sci U S A 93:9431-9436 (1996)
PubMed id: 8790347  
The mode of action and the structure of a herbicide in complex with its target: binding of activated hydantocidin to the feedback regulation site of adenylosuccinate synthetase.
R.Fonné-Pfister, P.Chemla, E.Ward, M.Girardet, K.E.Kreuz, R.B.Honzatko, H.J.Fromm, H.P.Schär, M.G.Grütter, S.W.Cowan-Jacob.
(+)-Hydantocidin, a recently discovered natural spironucleoside with potent herbicidal activity, is shown to be a proherbicide that, after phosphorylation at the 5' position, inhibits adenylosuccinate synthetase, an enzyme involved in de novo purine synthesis. The mode of binding of hydantocidin 5'-monophosphate to the target enzyme was analyzed by determining the crystal structure of the enzyme-inhibitor complex at 2.6-A resolution. It was found that adenylosuccinate synthetase binds the phosphorylated compound in the same fashion as it does adenosine 5'-monophosphate, the natural feedback regulator of this enzyme. This work provides the first crystal structure of a herbicide-target complex reported to date.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17942678 S.O.Duke (2007).
The emergence of grass root chemical ecology.
  Proc Natl Acad Sci U S A, 104, 16729-16730.  
16669783 R.Zrenner, M.Stitt, U.Sonnewald, and R.Boldt (2006).
Pyrimidine and purine biosynthesis and degradation in plants.
  Annu Rev Plant Biol, 57, 805-836.  
12654029 R.Boldt, and R.Zrenner (2003).
Purine and pyrimidine biosynthesis in higher plants.
  Physiol Plant, 117, 297-304.  
  9611179 D.Guyer, A.Tuttle, S.Rouse, S.Volrath, M.Johnson, S.Potter, J.Görlach, S.Goff, L.Crossland, and E.Ward (1998).
Activation of latent transgenes in Arabidopsis using a hybrid transcription factor.
  Genetics, 149, 633-639.  
  9568898 M.Gregoriou, M.E.Noble, K.A.Watson, E.F.Garman, T.M.Krulle, la Fuente, G.W.Fleet, N.G.Oikonomakos, and L.N.Johnson (1998).
The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding.
  Protein Sci, 7, 915-927.
PDB codes: 1a8i 2gpn
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