PDBsum entry: 1dj2

Ligase

PDB id: 1dj2

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

Protein chains

Q96529  (PURA_ARATH) -  Adenylosuccinate synthetase, chloroplastic

Seq: 490 a.a.

Struc: 429 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.4.4 - Adenylosuccinate synthase.
• 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 

• Cellular component: apoplast (5 terms)
• Biological process: response to cadmium ion (3 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.