9K06

Crystal structure of Pyrococcus abyssi AIR synthetase with residues 51-54 replaced by Neisseria gonorrhoeae residues 49-56

Summary for 9K06

• Entry DOI: 10.2210/pdb9k06/pdb
• Descriptor: Phosphoribosylformylglycinamidine cyclo-ligase, SULFATE ION, CITRATE ANION, ... (4 entities in total)
• Functional Keywords: purine synthesis, atp hydrolysis, ligase
• Biological source: Pyrococcus abyssi GE5
• Total number of polymer chains: 2
• Total formula weight: 72083.10

Authors

Chen, Y.H.,Chen, C.J. (deposition date: 2024-10-15, release date: 2025-10-15, Last modification date: 2026-02-11)

Primary citation

Chen, Y.H.,Huang, Y.C.,Rao, R.G.R.,Chang, H.C.,Lan, Y.H.,Nakagawa, A.,Jeyaraman, J.,Chen, C.J.
Structural insights into substrate binding, domain swapping and heat resistance of a hyperthermostable archaeal AIR synthetase.
Int.J.Biol.Macromol., 344:150493-150493, 2026

PubMed Abstract: The enzyme 5-aminoimidazole ribonucleotide synthetase (AIR synthetase, AIRS, known also as PurM) catalyzes the fifth step in the de novo purine biosynthetic pathway: the ATP-dependent conversion of formylglycinamidine ribonucleotide (FGAM) to aminoimidazole ribonucleotide (AIR). AIRS belongs to the PurM superfamily, sharing ATPase domains. In this study, we employed hyperthermostable AIRS from Pyrococcus abyssi (Pa) and Pyrococcus horikoshii (Ph), members of the thermophilic archaeal genus known for extreme heat tolerance, to resolve the substrate-binding site and structural features. Crystal structures of AIRS were determined in complex with the substrate analog formylglycinamide ribonucleotide (FGAR), the non-hydrolyzable ATP analog adenylyl-imidodiphosphate (AMPPNP), the product ADP, and metal cofactors (Mn, Mg, and K), respectively. AMPPNP and FGAR bind to the α1-β1 loop and the disordered N-terminal tail, respectively, stabilizing the active-site conformation. These findings provide a structural framework for understanding substrate positioning and catalysis within AIRS. A unique non-domain-swapping feature observed in the first 54 residues of the N-terminal domain in PaAIRS and PhAIRS, differing from their orthologs. The domain-swappable feature is found to be β1-β2 loop-dependent and can be categorized into two distinct types in the AIRS family: a short-looped, non-swapping archaeal type and a long-looped, swapping bacterial type. Structural, mutational, and biophysical analyses suggest that the thermostability is supported by enhanced hydrophobic core packing, strengthened dimer interfaces, and shortened surface loops. Collectively, these findings not only elucidate the substrate binding, the catalytic mechanism, and domain swapping of AIRS but also contribute to our understanding of the compact and robust architecture characteristics of thermophilic proteins.

PubMed: 41581817
DOI: 10.1016/j.ijbiomac.2026.150493

Experimental method

X-RAY DIFFRACTION (1.7 Å)