PDBsum entry: 1jqp

Hydrolase

PDB id: 1jqp

Contents

Protein chain

348 a.a. *

Ligands

NAG ×2

SO4

Metals

_CL

Waters ×83

* Residue conservation analysis

PDB id:

1jqp

Name:

Hydrolase

Title:

Dipeptidyl peptidase i (cathepsin c), a tetrameric cysteine of the papain family

Structure:

Dipeptidyl peptidase i. Chain: a. Synonym: cathepsin c. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.40Å R-factor: 0.245 R-free: 0.274

Authors:

J.G.Olsen,A.Kadziola,C.Lauritzen,J.Pedersen,S.Larsen,S.W.Dah

Key ref:

J.G.Olsen et al. (2001). Tetrameric dipeptidyl peptidase I directs substrate specificity by use of the residual pro-part domain. FEBS Lett, 506, 201-206. PubMed id: 11602245 DOI: 10.1016/S0014-5793(01)02911-8

Date:

08-Aug-01 Release date: 18-Oct-02

Protein chain

P80067  (CATC_RAT) -  Dipeptidyl peptidase 1

Seq: 462 a.a.

Struc: 348 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.14.1 - Dipeptidyl-peptidase I.
• Reaction: Release of an N-terminal dipeptide, Xaa-Xbb-|-Xcc, except when Xaa is Arg or Lys, or Xbb or Xcc is Pro.

 Gene Ontology (GO) functional annotation 

• Cellular component: endoplasmic reticulum (3 terms)
• Biological process: aging (3 terms)
• Biochemical function: hydrolase activity (7 terms)

DOI no: 10.1016/S0014-5793(01)02911-8

FEBS Lett 506:201-206 (2001)

PubMed id: 11602245

Tetrameric dipeptidyl peptidase I directs substrate specificity by use of the residual pro-part domain.

J.G.Olsen, A.Kadziola, C.Lauritzen, J.Pedersen, S.Larsen, S.W.Dahl.

ABSTRACT

The crystal structure of mature dipeptidyl peptidase I reveals insight into the unique tetrameric structure, substrate binding and activation of this atypical papain family peptidase. Each subunit is composed of three peptides. The heavy and light chains form the catalytic domain, which adopts the papain fold. The residual pro-part forms a beta-barrel with the carboxylate group of Asp1 pointing towards the substrate amino-terminus. The tetrameric structure appears to stabilize the association of the two domains and encloses a 12700 A3 spherical cavity. The tetramer contains six chloride ions, one buried in each S2 pocket and two at subunit interfaces.

Selected figure(s)

Figure 1.
Fig. 1. The fold and domain structure of DPPI. A: A ribbon trace of of the subunit which consists of three polypeptide chains in the activated enzyme: the 118 residue long residual pro-part to the left (shown in turquoise) and the heavy and light chains (shown in magenta and orange, respectively) which constitute the papain fold domain. The pale yellow spheres represent chloride ions. Active site residues Cys233 and His380 as well as N-acetylglucosamine residues and their associated asparagines are shown in ball-and-stick representation. B: The eight-stranded meander β-barrel residual pro-part domain is rainbow-colored such that residue 1 is blue and residue 118 is red. Chlorides are represented by pale yellow spheres and Asp1 and the active site nucleophile are shown in ball-and-stick representation. The papain fold core domain is shown in the background. C: The tetrameric structure of DPPI. Residual pro-part domains are shown in gray and the papain fold domain in red, yellow, blue, and green, representing the different subunits. The tetramer assembles around the crystallographic 2-fold axes with one subunit in the asymmetric unit. Figures were prepared in Molscript [28].

Figure 2.
Fig. 2. The DPPI active site. A: The catalytic residues Cys233 and His380 and the substrate binding Asp1 residue are shown in ball-and-stick. Also shown is the chloride ion positioned at the N-terminus of the distorted helix 3. B: Electron density map contoured at 1.2σ superimposed on the model around the active site/substrate binding cleft. Figures prepared in Molscript [28] and TURBO-FRODO [19].

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2001, 506, 201-206) copyright 2001.