PDBsum entry: 1g9k

Hydrolase

PDB id: 1g9k

Contents

Protein chain

455 a.a. *

Ligands

SO4

Metals

_ZN

_CA ×7

Waters ×355

* Residue conservation analysis

PDB id:

1g9k

Name:

Hydrolase

Title:

Crystal structure of a psychrophilic alkaline protease from pseudomonas tac ii 18

Structure:

Serralysin. Chain: a. Synonym: calcium and zinc dependent alkaline protease. Ec: 3.4.24.40

Source:

Pseudomonas. Organism_taxid: 286. Strain: tac ii 18

Biol. unit:

Trimer (from PQS)

Resolution:

1.96Å R-factor: 0.156 R-free: 0.187

Authors:

N.Aghajari,R.Haser

Key ref:

N.Aghajari et al. (2003). Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases. Proteins, 50, 636-647. PubMed id: 12577270 DOI: 10.1002/prot.10264

Date:

24-Nov-00 Release date: 14-Feb-03

Protein chain

O69771  (O69771_9PSED) -  Serralysin (Precursor)

Seq: 480 a.a.

Struc: 455 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.24.40 - Serralysin.
• Reaction: Preferential cleavage of bonds with hydrophobic residues in P1'.
• Cofactor: Zinc

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular space (2 terms)
• Biological process: proteolysis (1 term)
• Biochemical function: hydrolase activity (6 terms)

DOI no: 10.1002/prot.10264

Proteins 50:636-647 (2003)

PubMed id: 12577270

Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.

N.Aghajari, F.Van Petegem, V.Villeret, J.P.Chessa, C.Gerday, R.Haser, J.Van Beeumen.

ABSTRACT

Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. It is in general accepted that psychrophilic enzymes are more flexible to allow easy accommodation and transformation of the substrates at low energy costs. Here, we report the structures of two crystal forms of the alkaline protease from an Antarctic Pseudomonas species (PAP), solved to 2.1- and 1.96-A resolution, respectively. Comparative studies of PAP structures with mesophilic counterparts show that the overall structures are similar but that the conformation of the substrate-free active site in PAP resembles that of the substrate-bound region of the mesophilic homolog, with both an active-site tyrosine and a substrate-binding loop displaying a conformation as in the substrate-bound form of the mesophilic proteases. Further, a region in the catalytic domain of PAP undergoes a conformational change with a loop movement as large as 13 A, induced by the binding of an extra calcium ion. Finally, the active site is more accessible due to deletions occurring in surrounding loop regions.

Selected figure(s)

Figure 2.
Figure 2. (a) General overview of the structure of PAP. The N-terminal (catalytic) domain is blue and the C-terminal domain red. Calcium ions in the C-terminal domain are indicated as yellow spheres, the extra calcium in the N-terminal domain is purple, and the Zn ion green. A sulphate ion (only present in form 2) is shown in the catalytic domain as well. (b) Superposition of PAP form 1 (blue) and form 2 (cyan) with AP (red) and SMP (yellow). (a) and (b) were made using MOLSCRIPT.[45] (c) Representation of conserved regions coloured as degree of similarity with AP and serralysin (SMP), where red indicates highly conserved areas (drawing made using the program BOBSCRIPT[46]).

Figure 4.
Figure 4. (a) Zn^2+ coordination site of PAP form 1 with the Zn^2+ ion (grey sphere) coordinating three histidines (169, 173, and 179), a tyrosine (209), which has a double conformation, and a water molecule (red). (b) Superpositions of the active-site Tyr(209) and Zn^2+ of PAP (the two conformations for crystal form 1 in blue and one conformation for form 2 in green with corresponding unligated (red) and ligated (light brown) Tyr in AP.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 50, 636-647) copyright 2003.

Figures were selected by an automated process.