Structure of a ternary complex of proteinase K, mercury, and a substrate-analogue hexa-peptide at 2.2 A resolution.
The crystal structure of a ternary complex of proteinase K, Hg(II) and a hexapeptide N-Ac-Pro-Ala-Pro-Phe-Pro-Ala-NH2 has been determined at 2.2 A resolution and refined to an R factor of 0.172 for 12,910 reflections. The mercury atom occupies two alternate sites, each of which was assigned an occupancy of 0.45. These two sites are bridged by Cys-73 S gamma which forms covalent bonds to both. Both mercury sites form regular polyhedrons involving atoms from residues Asp-39, His-69, Cys-73, His-72, Met-225, and Wat-324. The complex formation with mercury seems to disturb the stereochemistry of the residues of the catalytic triad Asp-39, His-69, and Ser-224 appreciably, thus reducing the enzymatic activity of proteinase K to 15%. The electron density in the difference Fourier map shows that the hexapeptide occupies the S1 subsite predominantly and the standard recognition site constituted by Ser-132 to Gly-136 and Gly-100 to Tyr-104 segments is virtually empty. The hexapeptide is held firmly through a series of hydrogen bonds involving protein atoms and water molecules. As a result of complex formation, Asp-39, His-69, Met-225, Ile-220, Ser-219, Thr-223, and Ser-224 residues move appreciably to accommodate the mercury atoms and the hexapeptide. The largest movement is observed for Met-225 which is involved in multiple interactions with both mercury and the hexapeptide. The activity results indicate an inhibition rate of 95%, as a result of the combined effect of mercury and hexapeptide.
Saxena
A K
AK
Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
Singh
T P
TP
Peters
K
K
Fittkau
S
S
Visanji
M
M
Wilson
K S
KS
Betzel
C
C
D000577:Amides / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D003460:Crystallization; D018360:Crystallography, X-Ray; D019286:Endopeptidase K / Q000037:antagonists & inhibitors / Q000737:chemistry*; D006860:Hydrogen Bonding; D008628:Mercury / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D015842:Serine Proteinase Inhibitors / Q000737:chemistry*
D000577:Amides; D000596:Amino Acids; D009842:Oligopeptides; D015842:Serine Proteinase Inhibitors; D019286:Endopeptidase K; D008628:Mercury