2AYI

Wild-type AmpT from Thermus thermophilus

Summary for 2AYI

• Entry DOI: 10.2210/pdb2ayi/pdb
• Related: 1ZJC
• Descriptor: Aminopeptidase T, ZINC ION (2 entities in total)
• Functional Keywords: aminopeptidase, metallopeptidase, hydrolase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 5
• Total formula weight: 226054.15

Authors

Odintsov, S.G.,Sabala, I.,Bourenkov, G.,Rybin, V.,Bochtler, M. (deposition date: 2005-09-07, release date: 2005-11-08, Last modification date: 2023-08-23)

Primary citation

Odintsov, S.G.,Sabala, I.,Bourenkov, G.,Rybin, V.,Bochtler, M.
Substrate Access to the Active Sites in Aminopeptidase T, a Representative of a New Metallopeptidase Clan.
J.Mol.Biol., 354:403-412, 2005

PubMed Abstract: Aminopeptidase T (AmpT) from Thermus thermophilus is a metalloexopeptidase with no similarity to prototypical metallopeptidases with an HExxH or HxxEH motif. The crystal structure of the Staphylococcus aureus homologue of AmpT, which is known as aminopeptidase S (AmpS), has been reported recently. This structure revealed a dimeric protein with a very unusual, elongated shape and a large internal cavity. The active sites were found on the inner walls of the cavity and were entirely shielded from the environment, which suggested either that the dimer in the crystals was not physiologically relevant, or that an inactive conformation had been crystallized. Here, we show by gel-filtration and analytical ultracentrifugation that AmpT, like AmpS, forms dimers in solution, and we present the structure of AmpT in a crystal form with five protomers in the asymmetric unit. The five protomers take conformations that range from fully closed, as in the AmpS structure, to nearly open, so that the active site is almost directly accessible. The different conformations indicate flexibility between the AmpT N and C-domains, and explain how AmpT can be active, although the unusual AmpS dimerization mode applies to AmpT as well.

PubMed: 16242715
DOI: 10.1016/j.jmb.2005.09.042

Experimental method

X-RAY DIFFRACTION (3.7 Å)