PDBsum entry 1mir

Hydrolase

PDB id: 1mir

Contents

Protein chains

313 a.a. *

Waters ×99

* Residue conservation analysis

PDB id:

1mir

Name:

Hydrolase

Title:

Rat procathepsin b

Structure:

Procathepsin b. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Variant: naturally occurring variant v223a. Expressed in: pichia pastoris. Expression_system_taxid: 4922

Resolution:

2.80Å R-factor: 0.220 R-free: 0.270

Authors:

M.Cygler,J.Sivaraman,P.Grochulski,R.Coulombe,A.C.Storer,J.S.Mort

Key ref:

M.Cygler et al. (1996). Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion. Structure, 4, 405-416. PubMed id: 8740363 DOI: 10.1016/S0969-2126(96)00046-9

Date:

12-Jan-96 Release date: 11-Jan-97

Protein chains

P00787  (CATB_RAT) -  Cathepsin B from Rattus norvegicus

Seq: 339 a.a.

Struc: 313 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.22.1 - cathepsin B.
• Reaction: Hydrolysis of proteins with broad specificity for peptide bonds. Preferentially cleaves -Arg-Arg-|-Xaa bonds in small molecule substrates (thus differing from cathepsin L). In addition to being an endopeptidase, shows peptidyl-dipeptidase activity, liberating C-terminal dipeptides.

DOI no: 10.1016/S0969-2126(96)00046-9

Structure 4:405-416 (1996)

PubMed id: 8740363

Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion.

M.Cygler, J.Sivaraman, P.Grochulski, R.Coulombe, A.C.Storer, J.S.Mort.

ABSTRACT

BACKGROUND: Cysteine proteases of the papain superfamily are synthesized as inactive precursors with a 60-110 residue N-terminal prosegment. The propeptides are potent inhibitors of their parent proteases. Although the proregion binding mode has been elucidated for all other protease classes, that of the cysteine proteases remained elusive. RESULTS: We report the three-dimensional structure of rat procathepsin B, determined at 2.8 A resolution. The 62-residue proregion does not form a globular structure on its own, but folds along the surface of mature cathepsin B. The N-terminal part of the proregion packs against a surface loop, with Trp24p (p indicating the proregion) playing a pivotal role in these interactions. Inhibition occurs by blocking access to the active site: part of the proregion enters the substrate-binding cleft in a similar manner to a natural substrate, but in a reverse orientation. CONCLUSIONS: The structure of procathepsin B provides the first insight into the mode of interaction between a mature cysteine protease from the papain superfamily and its prosegment. Maturation results in only one loop of cathepsin B changing conformation significantly, replacing contacts lost by removal of the prosegment. Contrary to many other proproteases, no rearrangement of the N terminus occurs following activation. Binding of the prosegment involves interaction with regions of the enzyme remote from the substrate-binding cleft and suggests a novel strategy for inhibitor design. The region of the prosegment where the activating cleavage occurs makes little contact with the enzyme, leading to speculation on the activation mechanism.

Selected figure(s)

Figure 2.
Figure 2. Molecular surface of the mature portion of procathepsin B with the prosegment shown as a worm representation. The view is toward the active site. Figure 2. Molecular surface of the mature portion of procathepsin B with the prosegment shown as a worm representation. The view is toward the active site. (The figure was prepared using GRASP [[3]48].)

Figure 5.
Figure 5. Contacts between the prosegment and catB within the occluding-loop crevice. Hydrogen bonds are shown as dashed lines. The prosegment is drawn in dark lines. Figure 5. Contacts between the prosegment and catB within the occluding-loop crevice. Hydrogen bonds are shown as dashed lines. The prosegment is drawn in dark lines. (Figure was created using MOLSCRIPT [[3]47].)

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 405-416) copyright 1996.

Figures were selected by an automated process.