PDBsum entry 1mzd

Hydrolase

PDB id: 1mzd

Contents

Protein chain

240 a.a. *

Waters ×30

* Residue conservation analysis

PDB id:

1mzd

Name:

Hydrolase

Title:

Crystal structure of human pro-granzyme k

Structure:

Pro-granzyme k. Chain: a. Synonym: granzyme k, granzyme 3, nk-tryptase-2. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: bone marrow. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.90Å R-factor: 0.224 R-free: 0.317

Authors:

C.Hink-Schauer,E.Estebanez-Perpina,E.Wilharm,P.Fuentes-Prior, W.Klinkert,W.Bode,D.E.Jenne

Key ref:

C.Hink-Schauer et al. (2002). The 2.2-A crystal structure of human pro-granzyme K reveals a rigid zymogen with unusual features. J Biol Chem, 277, 50923-50933. PubMed id: 12384499 DOI: 10.1074/jbc.M207962200

Date:

07-Oct-02 Release date: 14-Jan-03

Protein chain

P49863  (GRAK_HUMAN) -  Granzyme K from Homo sapiens

Seq: 264 a.a.

Struc: 240 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1074/jbc.M207962200

J Biol Chem 277:50923-50933 (2002)

PubMed id: 12384499

The 2.2-A crystal structure of human pro-granzyme K reveals a rigid zymogen with unusual features.

C.Hink-Schauer, E.Estébanez-Perpiñá, E.Wilharm, P.Fuentes-Prior, W.Klinkert, W.Bode, D.E.Jenne.

ABSTRACT

Granzyme K (GzmK) belongs to a family of trypsin-like serine proteases localized in electron dense cytoplasmic granules of activated natural killer and cytotoxic T-cells. Like the related granzymes A and B, GzmK can trigger DNA fragmentation and is involved in apoptosis. We expressed the Ser(195) --> Ala variant of human pro-GzmK in Escherichia coli, crystallized it, and determined its 2.2-A x-ray crystal structure. Pro-GzmK possesses a surprisingly rigid structure, which is most similar to activated serine proteases, in particular complement factor D, and not their proforms. The N-terminal peptide Met(14)-Ile(17) projects freely into solution and can be readily approached by cathepsin C, the natural convertase of pro-granzymes. The pre-shaped S1 pocket is occupied by the ion paired residues Lys(188B)-Asp(194) and is hence not available for proper substrate binding. The Ser(214)-Cys(220) segment, which normally provides a template for substrate binding, bulges out of the active site and is distorted. With analogy to complement factor D, we suggest that this strand will maintain its non-productive conformation in mature GzmK, mainly due to the unusual residues Gly(215), Glu(219), and Val(94). We hypothesize that GzmK is proteolytically active only toward specific, as yet unidentified substrates, which upon approach transiently induce a functional active-site conformation.

Selected figure(s)

Figure 3.
Fig. 3. Solid surface representations of pro-GzmK. A, the molecule is rotated downward with respect to the standard orientation as shown in Fig. 1. B, pro-GzmK is further rotated by 180° around the x-axis. The colors indicate positive (blue) and negative (red) electrostatic potential at the molecular surface, contoured at +10 kT/e to 10 kT/e. Basic and acidic residues are highlighted by yellow labels consisting of single-letter symbols for amino acid residues and sequence numbers; the N and C termini of pro-GzmK are marked with yellow labels. The figure was made with GRASP (59).

Figure 6.
Fig. 6. Putative structure of active GzmK bound to a substrate/inhibitor. The crystal structure of pro-GzmK (blue) is shown superimposed with a model of active GzmK (red). In addition, the reactive site loop of the second Kunitz-type domain of bikunin (1BIK, residues Gly89-Phe^94, yellow) has been modeled into the active site region using the known complex between BPTI and trypsin as a template. The figure was prepared with WEBLABVIEWER (available at www.msi.com).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 50923-50933) copyright 2002.

Figures were selected by an automated process.