PDBsum entry 1nht

Ligase

PDB id: 1nht

Contents

Protein chain

431 a.a. *

Ligands

GDP

HDA

PGS

Metals

_MG

Waters ×1362

* Residue conservation analysis

PDB id:

1nht

Name:

Ligase

Title:

Entrapment of 6-thiophosphoryl-imp in the active site of crystalline adenylosuccinate synthetase from escherichia coli data collected at 100k

Structure:

Adenylosuccinate synthetase. Chain: a. Ec: 6.3.4.4

Source:

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

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.206 R-free: 0.255

Authors:

B.W.Poland,C.A.Bruns,H.J.Fromm,R.B.Honzatko

Key ref:

B.W.Poland et al. (1997). Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli. J Biol Chem, 272, 15200-15205. PubMed id: 9182542 DOI: 10.1074/jbc.272.24.15200

Date:

12-Jan-97 Release date: 08-Oct-97

Protein chain

P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase from Escherichia coli (strain K12)

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: IMP + L-aspartate + GTP = N₆-(1,2-dicarboxyethyl)-AMP + GDP + phosphate + 2 H⁺

IMP + L-aspartate + GTP (Bound ligand (Het Group name = HDA) matches with 41.67% similarity) = N(6)-(1,2-dicarboxyethyl)-AMP (Bound ligand (Het Group name = GDP) corresponds exactly) + GDP + phosphate + 2 × H(+)

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

reference

DOI no: 10.1074/jbc.272.24.15200

J Biol Chem 272:15200-15205 (1997)

PubMed id: 9182542

Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli.

B.W.Poland, C.Bruns, H.J.Fromm, R.B.Honzatko.

ABSTRACT

Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with Mg2+, 6-thiophosphoryl-IMP, GDP, and hadacidin at 298 and 100 K have been refined to R-factors of 0.171 and 0.206 against data to 2.8 and 2.5 A resolution, respectively. Interactions of GDP, Mg2+ and hadacidin are similar to those observed for the same ligands in the complex of IMP, GDP, NO3-, Mg2+ and hadacidin (Poland, B. W., Fromm, H. J. & Honzatko, R. B. (1996). J. Mol. Biol. 264, 1013-1027). Although crystals were grown from solutions containing 6-mercapto-IMP and GTP, the electron density at the active site is consistent with 6-thiophosphoryl-IMP and GDP. Asp-13 and Gln-224 probably work in concert to stabilize the 6-thioanion of 6-mercapto-IMP, which in turn is the nucleophile in the displacement of GDP from the gamma-phosphate of GTP. Once formed, 6-thiophosphoryl-IMP is stable in the active site of the enzyme under the conditions of the structural investigation. The direct observation of 6-thiophosphoryl-IMP in the active site is consistent with the putative generation of 6-phosphoryl-IMP along the reaction pathway of the synthetase.

Selected figure(s)

Figure 2.
Fig. 2. Stereo view of bound ligands in relation to a trace of -carbons of adenylosuccinate synthetase.

Figure 6.
Fig. 6. Proposed mechanism for the phosphotransfer reaction governed by the synthetase, involving 6-mercapto-IMP as a substrate. L-Aspartate is not shown here but is putatively coordinated to Mg2+ as shown in Fig. 7.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 15200-15205) copyright 1997.

Figures were selected by an automated process.