4WWV

Aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis

Summary for 4WWV

• Entry DOI: 10.2210/pdb4wwv/pdb
• Related: 1XFO 1Y0F
• Descriptor: Aminopeptidase from family M42 (2 entities in total)
• Functional Keywords: aminopeptidase, hydrolase
• Biological source: Desulfurococcus kamchatkensis
• Total number of polymer chains: 2
• Total formula weight: 86521.58

Authors

Petrova, T.,Boyko, K.M.,Rakitina, T.V.,Korzhenevskiy, D.A.,Gorbacheva, M.A.,Popov, V.O. (deposition date: 2014-11-12, release date: 2015-03-04, Last modification date: 2024-01-10)

Primary citation

Petrova, T.E.,Slutskaya, E.S.,Boyko, K.M.,Sokolova, O.S.,Rakitina, T.V.,Korzhenevskiy, D.A.,Gorbacheva, M.A.,Bezsudnova, E.Y.,Popov, V.O.
Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis.
Acta Crystallogr.,Sect.F, 71:277-285, 2015

PubMed Abstract: The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are similar.

PubMed: 25760701
DOI: 10.1107/S2053230X15000783

Experimental method

X-RAY DIFFRACTION (3.006 Å)