PDBsum entry: 1ade

Ligase (synthetase)

PDB id: 1ade

Contents

Protein chains

431 a.a. *

Waters ×1722

* Residue conservation analysis

PDB id:

1ade

Name:

Ligase (synthetase)

Title:

Structure of adenylosuccinate synthetase ph 7 at 25 degrees celsius

Structure:

Adenylosuccinate synthetase. Chain: a, b. Ec: 6.3.4.4

Source:

Escherichia coli. Organism_taxid: 562. Strain: pur a strain h1238. Other_details: coli genetic stock center, strain number 5408. Gift from dr. B. Bachman, genetic center, yale university

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.199

Authors:

M.M.Silva,B.W.Poland,C.M.Hoffman,H.J.Fromm,R.B.Honzatko

Key ref:

M.M.Silva et al. (1995). Refined crystal structures of unligated adenylosuccinate synthetase from Escherichia coli. J Mol Biol, 254, 431-446. PubMed id: 7490761 DOI: 10.1006/jmbi.1995.0629

Date:

14-Sep-95 Release date: 29-Jan-96

Protein chains

P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase

Seq: 432 a.a.

Struc: 431 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

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (2 terms)
• Biological process: nucleobase, nucleoside and nucleotide interconversion (3 terms)
• Biochemical function: nucleotide binding (7 terms)

reference

DOI no: 10.1006/jmbi.1995.0629

J Mol Biol 254:431-446 (1995)

PubMed id: 7490761

Refined crystal structures of unligated adenylosuccinate synthetase from Escherichia coli.

M.M.Silva, B.W.Poland, C.R.Hoffman, H.J.Fromm, R.B.Honzatko.

ABSTRACT

Crystal structures of unligated adenylosuccinate synthetase from Escherichia coli in space groups P2(1) and P2(1)2(1)2(1) have been refined to R-factors of 0.199 and 0.206 against data to 2.0 and 2.5 A, respectively. Bond lengths and angles deviate from expected values by 0.011 A and 1.7 degrees for the P2(1) crystal form and by 0.015 A and 1.7 degrees for the P2(1)2(1)2(1) crystal form. The fold of the polypeptide chain is dominated by a central beta-sheet, which is composed of nine parallel strands and a tenth antiparallel strand. Extending off from this central beta-sheet are four subdomains. The four subdomains contribute loops of residues that are disordered or have high thermal parameters. At least three of these loops (residues 42 to 52, 120 to 131 and 298 to 304) contribute essential residues to the putative active site of the synthetase. In the absence of ligands, much of the active site of the synthetase exists in an ill-defined conformational state. Two, nearly independent regions contribute residues to the interface between polypeptide chains of the synthetase dimer. A pair of helices (H4 and H5) interact with their symmetry-equivalent mates by way of residues that are not conserved amongst the known sequences of the synthetase. The second interface region involves conserved residues belonging to structural elements that connect strands of the central beta-sheet. Residues putatively involved in the binding of IMP lie at or near the interface between polypeptide chains of the dimer. Of the four sequence elements putatively common to all GTP hydrolases, the synthetase has only the guanine recognition element and a glycine-rich loop (P-loop). Although the base recognition element is essentially identical with those of the p21 ras and G alpha proteins, the P-loop of the synthetase is extended in size relative to the P-loops of other GTP hydrolases. The P-loop has two acid residues (Asp13 and Glu14), which are found in the P-loops of only the synthetase family. Glu14 may be involved in the stabilization of the enlarged P-loop of the synthetase, whereas Asp13 may play a role in catalysis and in the coordination of Mg2+. The structural elements of the p21 ras and G alpha proteins responsible for binding Mg2+ are either absent from the synthetase or unavailable for the coordination of metal cations.

Selected figure(s)

Figure 1.
Figure 1. Amino acid sequence used in the refinement of unligated crystal structures of the synthetase.

Figure 8.
Figure 8. Identification of the active site of the synthetase (top) by the location of IMP and GDP in a preliminary crystal structure, (middle) by directed mutation, and (bottom) by the mapping of conserved residues of synthetases from bacteria, yeast and mammals. Drawing by MOLSCRIPT (Kraulis, 1991).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 254, 431-446) copyright 1995.

Figures were selected by an automated process.