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

Yokoyama H, Hamamatsu S, Fujii S, Matsui I - J Synchrotron Radiat (2008)

Bottom Line: Two possible sets of dimer were found from the symmetry-related molecules.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.

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.

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Molecular surface of the type-1 dimer of 1510-N K138A viewed from almost the same direction as Fig. 2 ▶. Polar residues (Asp, Glu, His, Lys, Arg, Gly, Ser, Thr, Cys, Asn and Gln) are shown in green, and hydrophobic and aromatic residues are in white. Ser97 is shown in yellow and Ala138 is in red. The dashed circle indicates the hydrophobic region around the active site.
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fig4: Molecular surface of the type-1 dimer of 1510-N K138A viewed from almost the same direction as Fig. 2 ▶. Polar residues (Asp, Glu, His, Lys, Arg, Gly, Ser, Thr, Cys, Asn and Gln) are shown in green, and hydrophobic and aromatic residues are in white. Ser97 is shown in yellow and Ala138 is in red. The dashed circle indicates the hydrophobic region around the active site.

Mentions: In the K138A structure, the molecular surface representation indicates that the active site around S97 and A138 (mutated from Lys) is in a hydrophobic environment (Fig. 4 ▶). In particular, the aromatic residues Tyr101, Tyr142, Phe143 and Tyr146 form a cluster along with Met70 and Met71 (Fig. 5 ▶). The hydrophobic region is probably the binding site of hydrophobic substrates, and 1510-N preferentially degrades hydrophobic substrates in the region.


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

Yokoyama H, Hamamatsu S, Fujii S, Matsui I - J Synchrotron Radiat (2008)

Molecular surface of the type-1 dimer of 1510-N K138A viewed from almost the same direction as Fig. 2 ▶. Polar residues (Asp, Glu, His, Lys, Arg, Gly, Ser, Thr, Cys, Asn and Gln) are shown in green, and hydrophobic and aromatic residues are in white. Ser97 is shown in yellow and Ala138 is in red. The dashed circle indicates the hydrophobic region around the active site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394792&req=5

fig4: Molecular surface of the type-1 dimer of 1510-N K138A viewed from almost the same direction as Fig. 2 ▶. Polar residues (Asp, Glu, His, Lys, Arg, Gly, Ser, Thr, Cys, Asn and Gln) are shown in green, and hydrophobic and aromatic residues are in white. Ser97 is shown in yellow and Ala138 is in red. The dashed circle indicates the hydrophobic region around the active site.
Mentions: In the K138A structure, the molecular surface representation indicates that the active site around S97 and A138 (mutated from Lys) is in a hydrophobic environment (Fig. 4 ▶). In particular, the aromatic residues Tyr101, Tyr142, Phe143 and Tyr146 form a cluster along with Met70 and Met71 (Fig. 5 ▶). The hydrophobic region is probably the binding site of hydrophobic substrates, and 1510-N preferentially degrades hydrophobic substrates in the region.

Bottom Line: Two possible sets of dimer were found from the symmetry-related molecules.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.

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.

Show MeSH