3WG5

1510-N membrane-bound stomatin-specific protease K138A mutant in complex with a substrate peptide under heat treatment

Summary for 3WG5

• Entry DOI: 10.2210/pdb3wg5/pdb
• Related: 2DEO 3BPP 3VIV
• Descriptor: 441aa long hypothetical nfeD protein, PH1511 stomatin, GLYCEROL, ... (6 entities in total)
• Functional Keywords: protein-peptide complex, alpha/beta motif, protease, membrane protein stomatin, hydrolase-protein binding complex, hydrolase/protein binding
• Biological source: Pyrococcus horikoshii; More
• Total number of polymer chains: 3
• Total formula weight: 52321.42

Authors

Yokoyama, H.,Fujii, S.,Matsui, I. (deposition date: 2013-07-26, release date: 2013-10-23, Last modification date: 2023-11-08)

Primary citation

Yokoyama, H.,Kobayashi, D.,Takizawa, N.,Fujii, S.,Matsui, I.
Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease.
J.Synchrotron Radiat., 20:933-937, 2013

PubMed Abstract: Membrane-bound proteases are involved in various regulatory functions. The N-terminal region of PH1510p (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser-Lys dyad (Ser97 and Lys138), and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511p. In a form of human hemolytic anemia known as hereditary stomatocytosis, the stomatin protein is deficient in the erythrocyte membrane due to mis-trafficking. In order to understand the catalytic mechanism of 1510-N in more detail, here the structural and biochemical analysis of 1510-N is reported. Two degraded products were produced via acyl-enzyme intermediates. 1510-N is a thermostable protease, and thus crystallization after heat treatment of the protease-peptide complex was attempted in order to understand the catalytic mechanism of 1510-N. The structure after heat treatment is almost identical to that with no heat treatment. According to the superposition between the structures with heat treatment and with no heat treatment, the N-terminal half of the peptide is superposed well, whereas the C-terminal half of the peptide is slightly deviated. The N-terminal half of the peptide binds to 1510-N more tightly than the C-terminal half of the peptide. The flexible L2 loops of 1510-N cover the peptide, and are involved in the protease activity.

PubMed: 24121343
DOI: 10.1107/S0909049513021328

Experimental method

X-RAY DIFFRACTION (2.4 Å)