PDBsum entry 2b6n

Hydrolase

PDB id: 2b6n

Contents

Protein chain

278 a.a. *

Ligands

ALA-PRO-THR

SO4 ×2

Metals

_CA

Waters ×210

* Residue conservation analysis

PDB id:

2b6n

Name:

Hydrolase

Title:

The 1.8 a crystal structure of a proteinase k like enzyme from a psychrotroph serratia species

Structure:

Proteinase k. Chain: a. Fragment: residues 1-277. Engineered: yes. Tripeptide. Chain: b. Engineered: yes

Source:

Serratia sp.. Organism_taxid: 348903. Strain: gf96. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the peptide is assumed to be a proteolysis product either from the expression or purification process.

Resolution:

1.80Å R-factor: 0.163 R-free: 0.194

Authors:

R.Helland,A.N.Larsen,A.O.Smalas,N.P.Willassen

Key ref:

R.Helland et al. (2006). The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species. FEBS J, 273, 61-71. PubMed id: 16367748 DOI: 10.1111/j.1742-4658.2005.05040.x

Date:

03-Oct-05 Release date: 07-Mar-06

Protein chain

Q3HUQ2  (Q3HUQ2_9GAMM) -  Proteinase K from Serratia sp. GF96

Seq: 629 a.a.

Struc: 278 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1111/j.1742-4658.2005.05040.x

FEBS J 273:61-71 (2006)

PubMed id: 16367748

The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.

R.Helland, A.N.Larsen, A.O.Smalås, N.P.Willassen.

ABSTRACT

Proteins from organisms living in extreme conditions are of particular interest because of their potential for being templates for redesign of enzymes both in biotechnological and other industries. The crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species has been solved to 1.8 A. The structure has been compared with the structures of proteinase K from Tritirachium album Limber and Vibrio sp. PA44 in order to reveal structural explanations for differences in biophysical properties. The Serratia peptidase shares around 40 and 64% identity with the Tritirachium and Vibrio peptidases, respectively. The fold of the three enzymes is essentially identical, with minor exceptions in surface loops. One calcium binding site is found in the Serratia peptidase, in contrast to the Tritirachium and Vibrio peptidases which have two and three, respectively. A disulfide bridge close to the S2 site in the Serratia and Vibrio peptidases, an extensive hydrogen bond network in a tight loop close to the substrate binding site in the Serratia peptidase and different amino acid sequences in the S4 sites are expected to cause different substrate specificity in the three enzymes. The more negative surface potential of the Serratia peptidase, along with a disulfide bridge close to the S2 binding site of a substrate, is also expected to contribute to the overall lower binding affinity observed for the Serratia peptidase. Clear electron density for a tripeptide, probably a proteolysis product, was found in the S' sites of the substrate binding cleft.

Selected figure(s)

Figure 1.
Fig. 1. Structural alignment of SPRK, PRK and VPRK. Helices (red tubes) and sheets (yellow arrows) are according to SPRK. Residues belonging to the S1 site are shaded blue and residues belonging to the S4 site are shaded light blue. *represents residues that are involved both in the S1 and S4 sites. Residues forming the calcium binding site found in SPRK (and VPRK) are shaded green, residues forming the ‘strong’ calcium binding site in PRK (and in VPRK) are shaded khaki, and residues forming the calcium sites unique for either PRK or VPRK are shaded pale green.

Figure 5.
Fig. 5. Stereo plot illustrating the tight loop forming the S2 binding site. Red is SPRK, green is PRK and blue is VPRK. Labels and distances in the loop refer to SPRK. The stabilizing hydrogen bonding network formed by residues Asn97, Ser99 and Ser101 in SPRK is displayed as ball-and-stick models. A similar network is not as strong in PRK and VPRK due to a shorter Ser97 in VPRK and a too-long Asn99 in PRK. The loop is anchored to the rest of the molecule in SPRK and VPRK by a disulfide bridge between Cys98 and Cys66 (Asp98 in PRK). The catalytic His69 is displayed as ball-and-stick model in order to illustrate the orientation of the loop relative to the binding site.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2006, 273, 61-71) copyright 2006.

Figures were selected by the author.