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PDBsum entry 1hon

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protein ligands Protein-protein interface(s) links
Ligase (synthetase) PDB id
1hon
Jmol
Contents
Protein chains
431 a.a. *
Ligands
GNH
Waters ×1158
* Residue conservation analysis
PDB id:
1hon
Name: Ligase (synthetase)
Title: Structure of guanine nucleotide (gppcp) complex of adenylosuccinate synthetase from escherichia coli at ph 6.5 and 25 degree celsius
Structure: Adenylosuccinate synthetase. Chain: a, b. Engineered: yes. Other_details: native p212121 crystals were soaked with gppnp+mg(+2)
Source: Escherichia coli. Organism_taxid: 562. Strain: h1238
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.186     R-free:   0.230
Authors: B.W.Poland,Z.Hou,C.Bruns,H.J.Fromm,R.B.Honzatko
Key ref:
B.W.Poland et al. (1996). Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli. J Biol Chem, 271, 15407-15413. PubMed id: 8663109 DOI: 10.1074/jbc.271.26.15407
Date:
26-Apr-96     Release date:   08-Nov-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.6.3.4.4  - Adenylosuccinate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
AMP and GMP Biosynthesis
      Reaction: GTP + IMP + L-aspartate = GDP + phosphate + N6-(1,2-dicarboxyethyl)- AMP
GTP
+ IMP
+ L-aspartate
=
GDP
Bound ligand (Het Group name = GNH)
matches with 93.00% similarity
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.271.26.15407 J Biol Chem 271:15407-15413 (1996)
PubMed id: 8663109  
 
 
Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli.
B.W.Poland, Z.Hou, C.Bruns, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
Structures of adenylosuccinate synthetase from Escherichia coli complexed with guanosine-5'-(beta,gamma-imido) triphosphate and guanosine-5'-(beta,gamma-methylene)triphosphate in the presence and the absence of Mg2+ have been refined to R-factors below 0.2 against data to a nominal resolution of 2.7 A. Asp333 of the synthetase hydrogen bonds to the exocyclic 2-amino and endocyclic N1 groups of the guanine nucleotide base, whereas the hydroxyl of Ser414 and the backbone amide of Lys331 hydrogen bond to the 6-oxo position. The side chains of Lys331 and Pro417 pack against opposite faces of the guanine nucleotide base. The synthetase recognizes neither the N7 position of guanine nucleotides nor the ribose group. Electron density for the guanine-5'-(beta,gamma-imido) triphosphate complex is consistent with a mixture of the triphosphate nucleoside and its hydrolyzed diphosphate nucleoside bound to the active site. The base, ribose, and alpha-phosphate positions overlap, but the beta-phosphates occupy different binding sites. The binding of guanosine-5'-(beta,gamma-methylene)triphosphate to the active site is comparable with that of guanosine-5'-(beta, gamma-imido)triphosphate. No electron density, however, for the corresponding diphosphate nucleoside is observed. In addition, electron density for bound Mg2+ is absent in these nucleotide complexes. The guanine nucleotide complexes of the synthetase are compared with complexes of other GTP-binding proteins and to a preliminary structure of the complex of GDP, IMP, Mg2+, and succinate with the synthetase. The enzyme, under conditions reported here, does not undergo a conformational change in response to the binding of guanine nucleotides, and minimally IMP and/or Mg2+ must be present in order to facilitate the complete recognition of the guanine nucleotide by the synthetase.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereoview of GppCp (bold lines) at its site of ligation to adenylosuccinate synthetase. Top, an overview representing the protein as a trace of its -carbons. Bottom, a detailed view of the region of binding of the guanine nucleotide.
Figure 3.
Fig. 3. Superposition of GppN, GppNp, and GppCp in the conformations observed for these nucleotides in their ligand complexes with the synthetase.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1996, 271, 15407-15413) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
10231526 P.Lee, A.Gorrell, H.J.Fromm, and R.F.Colman (1999).
Implication of arginine-131 and arginine-303 in the substrate site of adenylosuccinate synthetase of Escherichia coli by affinity labeling with 6-(4-bromo-2,3-dioxobutyl)thioadenosine 5'-monophosphate.
  Biochemistry, 38, 5754-5763.  
8961938 B.W.Poland, S.F.Lee, M.V.Subramanian, D.L.Siehl, R.J.Anderson, H.J.Fromm, and R.B.Honzatko (1996).
Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin.
  Biochemistry, 35, 15753-15759.
PDB code: 1juy
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