PDBsum entry 1af4

Serine protease

PDB id: 1af4

Contents

Protein chain

274 a.a. *

Ligands

DIO ×7

Metals

_CA

Waters ×65

* Residue conservation analysis

PDB id:

1af4

Name:

Serine protease

Title:

Crystal structure of subtilisin carlsberg in anhydrous dioxane

Structure:

Subtilisin carlsberg. Chain: a. Ec: 3.4.21.62

Source:

Bacillus licheniformis. Organism_taxid: 1402

Resolution:

2.60Å R-factor: 0.161 R-free: 0.248

Authors:

J.L.Schmitke,L.J.Stern,A.M.Klibanov

Key ref:

J.L.Schmitke et al. (1997). The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile. Proc Natl Acad Sci U S A, 94, 4250-4255. PubMed id: 9113975 DOI: 10.1073/pnas.94.9.4250

Date:

21-Mar-97 Release date: 16-Jun-97

Protein chain

P00780  (SUBC_BACLI) -  Subtilisin Carlsberg from Bacillus licheniformis

Seq: 379 a.a.

Struc: 274 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.62 - subtilisin.
• Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.

DOI no: 10.1073/pnas.94.9.4250

Proc Natl Acad Sci U S A 94:4250-4255 (1997)

PubMed id: 9113975

The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile.

J.L.Schmitke, L.J.Stern, A.M.Klibanov.

ABSTRACT

The x-ray crystal structure of the serine protease subtilisin Carlsberg in anhydrous dioxane has been determined to 2.6-A resolution. The enzyme structure is found to be nearly indistinguishable from the structures previously determined in water and acetonitrile. Small changes in the side-chain conformations between the dioxane and water structures are of the same magnitude as those observed between two structures in different aqueous systems. Seven enzyme-bound dioxane molecules have been detected, each potentially forming at least one hydrogen bond with a subtilisin hydrogen-bond donor or bound water. Two of the bound dioxane molecules are in the active-site region, one in the P2 and another bridging the P1' and P3' pockets. The other five dioxane molecules are located on the surface of subtilisin at interprotein crystal contacts. The locations of the bound solvent in the dioxane structure are distinct from those in the structures in acetonitrile and in water.

Selected figure(s)

Figure 3.
Fig. 3. (A) Refined crystallographic B factors (residue average) of subtilisin Carlsberg in dioxane (solid line), water (dashed line), and acetonitrile (dotted line). The difference in the exposed^ surface areas of subtilisin between dioxane and water (B) and^ between acetonitrile and water (C). As in Fig. 2, Ser-159 and^ Gly-160 are left out in A and B.

Figure 4.
Fig. 4. Active site of subtilisin Carlsberg in anhydrous dioxane compared with that in water (A) and acetonitrile (B). The catalytic^ triad, Asn-155 of the oxyanion hole (OH), and solvent molecules in the dioxane structure are shown as balls-and-sticks with carbon, oxygen, and nitrogen shown in white, light-gray, and black, respectively. The water molecules in the aqueous and acetonitrile structures are depicted as dark-gray balls in A and B. The acetonitrile molecules in that structure (B) are also shown as linear balls-and-sticks. The surface of the protein [Connolly algorithm (20)] in the^ active-site region in the dioxane structure is portrayed by black dots.

Figures were selected by an automated process.