8ORK

cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus

This is a non-PDB format compatible entry.

Summary for 8ORK

• Entry DOI: 10.2210/pdb8ork/pdb
• Descriptor: Cyclic 2,3-diphosphoglycerate synthetase, 3[N-MORPHOLINO]PROPANE SULFONIC ACID, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: synthetase, extremolyte, thermophilic, ligase
• Biological source: Methanothermus fervidus DSM 2088
• Total number of polymer chains: 1
• Total formula weight: 53344.15

Authors

De Rose, S.A.,Isupov, M. (deposition date: 2023-04-14, release date: 2023-12-06, Last modification date: 2024-11-13)

Primary citation

De Rose, S.A.,Isupov, M.N.,Worthy, H.L.,Stracke, C.,Harmer, N.J.,Siebers, B.,Littlechild, J.A.
Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus .
Front Microbiol, 14:1267570-1267570, 2023

PubMed Abstract: The enzyme cyclic di-phosphoglycerate synthetase that is involved in the production of the osmolyte cyclic 2,3-diphosphoglycerate has been studied both biochemically and structurally. Cyclic 2,3-diphosphoglycerate is found exclusively in the hyperthermophilic archaeal methanogens, such as , , and . Its presence increases the thermostability of archaeal proteins and protects the DNA against oxidative damage caused by hydroxyl radicals. The cyclic 2,3-diphosphoglycerate synthetase enzyme has been crystallized and its structure solved to 1.7 Å resolution by experimental phasing. It has also been crystallized in complex with its substrate 2,3 diphosphoglycerate and the co-factor ADP and this structure has been solved to 2.2 Å resolution. The enzyme structure has two domains, the core domain shares some structural similarity with other NTP-dependent enzymes. A significant proportion of the structure, including a 127 amino acid N-terminal domain, has no structural similarity to other known enzyme structures. The structure of the complex shows a large conformational change that occurs in the enzyme during catalytic turnover. The reaction involves the transfer of the γ-phosphate group from ATP to the substrate 2,3 -diphosphoglycerate and the subsequent S2 attack to form a phosphoanhydride. This results in the production of the unusual extremolyte cyclic 2,3 -diphosphoglycerate which has important industrial applications.

PubMed: 38045033
DOI: 10.3389/fmicb.2023.1267570

Experimental method

X-RAY DIFFRACTION (1.64 Å)