PDBsum entry 1pj8

Hydrolase/hydrolase substrate

PDB id: 1pj8

Contents

Protein chain

279 a.a. *

Ligands

PRO-ALA-PRO-PHE

PRO-ALA-NH2

Metals

_HG ×2

Waters ×179

* Residue conservation analysis

PDB id:

1pj8

Name:

Hydrolase/hydrolase substrate

Title:

Structure of a ternary complex of proteinase k, mercury and a substrate-analogue hexapeptide at 2.2 a resolution

Structure:

Proteinase k. Chain: a. Synonym: tritirachium alkaline proteinase, endopeptidase k. 6-residue peptide (n-ac-papfpa-nh2). Chain: i. Engineered: yes

Source:

Engyodontium album. Organism_taxid: 37998. Strain: limber. Synthetic: yes. Other_details: the peptide was chemically synthesized using solution phase synthesis

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.170

Authors:

A.K.Saxena,T.P.Singh,K.Peters,S.Fittkau,M.Visanji,K.S.Wilson,C.Betzel

Key ref:

A.K.Saxena et al. (1996). Structure of a ternary complex of proteinase K, mercury, and a substrate-analogue hexa-peptide at 2.2 A resolution. Proteins, 25, 195-201. PubMed id: 8811735

Date:

02-Jun-03 Release date: 17-Jun-03

Protein chain

P06873  (PRTK_PARAQ) -  Proteinase K from Parengyodontium album

Seq: 384 a.a.

Struc: 279 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.64 - peptidase K.
• Reaction: Hydrolysis of keratin and of other proteins, with subtilisin-like specificity. Hydrolyzes peptides amides.

Proteins 25:195-201 (1996)

PubMed id: 8811735

Structure of a ternary complex of proteinase K, mercury, and a substrate-analogue hexa-peptide at 2.2 A resolution.

A.K.Saxena, T.P.Singh, K.Peters, S.Fittkau, M.Visanji, K.S.Wilson, C.Betzel.

ABSTRACT

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.