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PDBsum entry 1dj2

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protein ligands Protein-protein interface(s) links
Ligase PDB id
1dj2
Jmol
Contents
Protein chains
429 a.a. *
Ligands
GDP ×2
* Residue conservation analysis
PDB id:
1dj2
Name: Ligase
Title: Structures of adenylosuccinate synthetase from triticum aestivum and arabidopsis thaliana
Structure: Adenylosuccinate synthetase. Chain: a, b. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.90Å     R-factor:   0.233     R-free:   0.273
Authors: L.Prade,S.W.Cowan-Jacob,P.Chemla,S.Potter,E.Ward,R.Fonne- Pfister
Key ref:
L.Prade et al. (2000). Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana. J Mol Biol, 296, 569-577. PubMed id: 10669609 DOI: 10.1006/jmbi.1999.3473
Date:
01-Dec-99     Release date:   24-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q96529  (PURA_ARATH) -  Adenylosuccinate synthetase, chloroplastic
Seq:
Struc:
490 a.a.
429 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 = GDP)
corresponds exactly
+ 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     apoplast   6 terms 
  Biological process     'de novo' AMP biosynthetic process   6 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.3473 J Mol Biol 296:569-577 (2000)
PubMed id: 10669609  
 
 
Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana.
L.Prade, S.W.Cowan-Jacob, P.Chemla, S.Potter, E.Ward, R.Fonne-Pfister.
 
  ABSTRACT  
 
Catalyzing the first step in the de novo synthesis of adenylmonophosphate, adenylosuccinate synthetase (AdSS) is a known target for herbicides and antibiotics. We have purified and crystallized recombinant AdSS from Arabidopsis thaliana and Tritium aestivum, expressed in Escherichia coli. The structures of A. thaliana and T. aestivum AdSS in complex with GDP were solved at 2.9 A and 3.0 A resolution, respectively. Comparison with the known structures from E. coli reveals that the overall fold is very similar to that of the E. coli protein. The longer N terminus in the plant sequences is at the same place as the longer C terminus of the E. coli sequence in the 3D structure. The GDP-binding sites have one additional hydrogen-bonding partner, which is a plausible explanation for the lower K(m) value. Due to its special position, this partner may also enable GTP to initiate a conformational change, which was, in E. coli AdSS, exclusively activated by ligands at the IMP-binding site. The dimer interfaces show up to six hydrogen bonds and six salt-bridges more than in the E. coli structure, although the contact areas have approximately the same size.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Ribbon diagram of the monomers of (a) A. thaliana and (b) T. aestivum AdSS. Helices are shown in red, sheets in blue and loops in orange. The N and C termini are in the middle of the right side. The monomers are perpendicular to the orientation in Figure 2. (c) Overlay of the monomers of E. coli (gray), T. aestivum (yellow) and A. thaliana (green) in the same orientation as in (a) and (b).
Figure 5.
Figure 5. (a) Overlay of the GDP-binding sites of T. aestivum and A. thaliana AdSS. All parts from A. thaliana are shown in green, all residues of T. aestivum in yellow and the GDP moiety of T. aestivum in standard colors. (b) Overlay of the GDP-binding sites of T. aestivum and E. coli AdSS. All residues of T. aestivum AdSS are shown in yellow. All parts from E. coli AdSS are shown in standard colors.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 569-577) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
12482871 T.Borza, C.V.Iancu, E.Pike, R.B.Honzatko, and H.J.Fromm (2003).
Variations in the response of mouse isozymes of adenylosuccinate synthetase to inhibitors of physiological relevance.
  J Biol Chem, 278, 6673-6679.  
12004071 C.V.Iancu, T.Borza, H.J.Fromm, and R.B.Honzatko (2002).
IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase.
  J Biol Chem, 277, 26779-26787.
PDB codes: 1iwe 1lny 1lon 1loo
11741996 Z.Hou, W.Wang, H.J.Fromm, and R.B.Honzatko (2002).
IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli.
  J Biol Chem, 277, 5970-5976.
PDB codes: 1kjx 1kkb 1kkf
11560929 C.V.Iancu, T.Borza, J.Y.Choe, H.J.Fromm, and R.B.Honzatko (2001).
Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure.
  J Biol Chem, 276, 42146-42152.
PDB code: 1j4b
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