PDBsum entry 2id4

Hydrolase/hydrolase inhibitor

PDB id: 2id4

Contents

Protein chains

480 a.a.

Ligands

ACE-ARG-GLU-ARG-LYK-0QE ×2

NAG-NDG ×2

NAG ×2

MLA

Metals

_NA ×2

_CA ×4

Waters ×711

References listed in PDB file

Key reference

Title

Differential p1 arginine and lysine recognition in the prototypical proprotein convertase kex2.

Authors

J.L.Wheatley, T.Holyoak.

Ref.

Proc Natl Acad Sci U S A, 2007, 104, 6626-6631. [DOI no: 10.1073/pnas.0701983104]

PubMed id

17426142

Abstract

The high-resolution crystal structure of kexin (Kex2) in complex with a peptidyl-chloromethylketone inhibitor containing a noncognate lysine at the P(1) position provides the structural basis for the differential lysine/arginine selectivity that defines the prohormone (proprotein) convertase (PC) family. By comparison with the previous structures of Kex2 and furin, this structure of the acylated enzyme provides a basis for the observed decrease in the acylation rate with substrates containing a lysine at P(1) and the absence of an effect on the deacylation rate without involving mobility of the S(1) lid. The structure of the complex shows that a secondary subsite in the S(1) pocket is present, and that this site recognizes and binds the P(1) lysine in a more shallow fashion than arginine. This results in a displacement of the bound peptide away from the S385 nucleophile relative to substrates containing a P(1) arginine. It is concluded that this alternate binding site and resultant displacement of the scissile bond in the active site results in the observed decrease in the acylation rate. Studies of the inactivation kinetics of Kex2 by two peptidyl chloromethylketone inhibitors demonstrates that the selectivity between lysine and arginine at the P(1) position arises at the acylation step, consistent with what was observed with peptidyl substrates [Rockwell NC, Fuller RS (2001) J Biol Chem 276:38394-38399].

Figure 2.
Fig. 2. Interactions between the P[1] lysine residue and the S[1]-binding pocket. The S[1] residues P275, D277, and D325 and the P[1] lysine are displayed as green ball-and-stick models. The S[1] calcium ion and the coordinating water molecule are rendered as gray and red spheres, respectively. The distances between the S[1] residues and the P[1] lysine side chain are indicated with dashed lines. The distances among the atoms are a = 2.75, b = 2.81, c = 3.73, d = 2.82, and e = 2.72 Å. 2F[o] – F[c] density rendered at 2.0 for the P[1] lysine, H213, and S385 is shown as a blue mesh.

Figure 3.
Fig. 3. The interactions between the P[2] arginine residue and the S[2]-binding pocket. The S[2] residues D176, D210, and D211 and the P[2] arginine are displayed as green ball-and-stick models. The distances between the S[2] residues and the P[2] arginine side chain are indicated with dashed lines, and the distance between the atoms is given in angstroms. 2F[o] – F[c] density rendered at 2.0 for the P[2] arginine is shown as a blue mesh.