PDBsum entry 1cnm

Hydrolase

PDB id: 1cnm

Contents

Protein chain

279 a.a. *

Ligands

CCN ×3

Metals

_CA ×2

Waters ×135

* Residue conservation analysis

PDB id:

1cnm

Name:

Hydrolase

Title:

Enhancement of catalytic efficiency of proteinase k through exposure to anhydrous organic solvent at 70 degrees celsius

Structure:

Protein (proteinase k). Chain: a. Ec: 3.4.21.64

Source:

Engyodontium album. Organism_taxid: 37998. Strain: limber

Resolution:

2.20Å R-factor: 0.168 R-free: 0.231

Authors:

M.N.Gupta,R.Tyagi,S.Sharma,S.Karthikeyan,T.P.Singh

Key ref:

M.N.Gupta et al. (2000). Enhancement of catalytic efficiency of enzymes through exposure to anhydrous organic solvent at 70 degrees C. Three-dimensional structure of a treated serine proteinase at 2.2 A resolution. Proteins, 39, 226-234. PubMed id: 10737944 DOI: 10.1002/(SICI)1097-0134(20000515)39:3<226::AID-PROT50>3.0.CO;2-Y

Date:

20-May-99 Release date: 27-May-99

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.

DOI no: 10.1002/(SICI)1097-0134(20000515)39:3<226::AID-PROT50>3.0.CO;2-Y

Proteins 39:226-234 (2000)

PubMed id: 10737944

Enhancement of catalytic efficiency of enzymes through exposure to anhydrous organic solvent at 70 degrees C. Three-dimensional structure of a treated serine proteinase at 2.2 A resolution.

M.N.Gupta, R.Tyagi, S.Sharma, S.Karthikeyan, T.P.Singh.

ABSTRACT

The enzyme behavior in anhydrous media has important applications in biotechnology. So far chemical modifications and protein engineering have been used to alter the catalytic power of the enzymes. For the first time, it is demonstrated that an exposure of enzyme to anhydrous organic solvents at optimized high temperature enhances its catalytic power through local changes at the binding region. Six enzymes: proteinase K, wheat germ acid phosphatase, alpha-amylase, beta-glucosidase, chymotrypsin and trypsin have been exposed to acetonitrile at 70 degrees C for three hours. The activities of these enzymes were found to be considerably enhanced. In order to understand the basis of this change in the activity of these enzymes, the structure of one of these treated enzymes, proteinase K has been analyzed in detail using X-ray diffraction method. The overall structure of the enzyme is similar to the native structure in aqueous environment. The hydrogen bonding system of the catalytic triad is intact after the treatment. However, the water structure in the substrate binding site undergoes some rearrangement as some of the water molecules are either displaced or completely absent. The most striking observation concerning the water structure pertains to the complete deletion of the water molecule which occupied the position at the so-called oxyanion hole in the active site of the native enzyme. Three acetonitrile molecules were found in the present structure. All the acetonitrile molecules are located in the recognition site. The sites occupied by acetonitrile molecules are independent of water molecules. The acetonitrile molecules are involved in extensive interactions with the protein atoms. All of them are interlinked through water molecules. The methyl group of one of the acetonitrile molecules (CCN1) interacts simultaneously with the hydrophobic side chains of Leu-96, Ile-107, and Leu-133. The development of such a hydrophobic environment at the recognition site introduces a striking conformation change in Ile-107 by rotating its side chain about C(alpha)--C(beta) bond by 180 degrees to bring about the delta-methyl group within the range of attractive van der Waals interactions with the methyl group of CCN1. A similar change has earlier been observed in proteinase K when it is complexed to a substrate analog lactoferrin fragment.

Selected figure(s)

Figure 4.
Figure 4. C[ ]tracing of the protein structure of treated proteinase K. Ball and stick model of acetonitrile with bound water molecules (black balls).

Figure 10.
Figure 10. The normal hydrogen bonding distances between the residues of the catalytic triad showing that the exposure of the enzyme to acetonitrile at 70°C for three hours and subsequently location of three acetonitrile molecules at the binding site did not affect the hydrogen bonding distances.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 39, 226-234) copyright 2000.

Figures were selected by an automated process.