PDBsum entry 3bpp

Hydrolase

PDB id: 3bpp

Contents

Protein chain

216 a.a.

Waters ×63

References listed in PDB file

Key reference

Title

Novel dimer structure of a membrane-Bound protease with a catalytic ser-Lys dyad and its linkage to stomatin.

Authors

H.Yokoyama, S.Hamamatsu, S.Fujii, I.Matsui.

Ref.

J Synchrotron Radiat, 2008, 15, 254-257.

PubMed id

18421152

Abstract

Membrane-bound proteases are involved in various regulatory functions. A previous report indicates that the N-terminal region of PH1510 (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 PH1511. According to the crystal structure of the wild-type 1510-N in dimeric form, the active site around Ser97 is in a hydrophobic environment suitable for the hydrophobic substrates. This article reports the crystal structure of the K138A mutant of 1510-N at 2.3 A resolution. The determined structure contains one molecule per asymmetric unit, but 1510-N is active in dimeric form. Two possible sets of dimer were found from the symmetry-related molecules. One dimer is almost the same as the wild-type 1510-N. Another dimer is probably in an inactive form. The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2.

Secondary reference #1

Title

Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon pyrococcus horikoshii.

Authors

H.Yokoyama, E.Matsui, T.Akiba, K.Harata, I.Matsui.

Ref.

J Mol Biol, 2006, 358, 1152-1164. [DOI no: 10.1016/j.jmb.2006.02.052]

PubMed id

16574150

Figure 1.
Figure 1. Stereo representation of the 2F[o] -F[c] electron densities around the active site of one monomer (chain B) of 1510-N. The densities are contoured at 1.0s. Each residue is shown as a stick model (C atom, yellow; N atom, blue; O atom, red; S atom, orange), and a catalytic residue Ser97 is shown in magenta stick.

Figure 3.
Figure 3. Stereo drawing of the interface of the 1510-N dimer viewed from the same direction as Figure 2(a). A non-crystallographic 2-fold axis relating the two monomers runs vertically in the Figure plane. Ribbon representations of b1, a7, and b9 are shown in gray. Major residues around the interface are depicted with yellow (chain B) and gray (chain A) sticks. Red and gray balls indicate water molecules. Broken lines show the hydrogen bonds. Each residue of chain B at the interface is labeled.

The above figures are reproduced from the cited reference with permission from Elsevier