PDBsum entry 1kug

Hydrolase/hydrolase inhibitor

PDB id: 1kug

Contents

Protein chain

201 a.a. *

Ligands

PCA-ASN-TRP

Metals

_CD ×11

Waters ×630

* Residue conservation analysis

PDB id:

1kug

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of a taiwan habu venom metalloproteinase complexed with its endogenous inhibitor penw

Structure:

Metalloproteinase. Chain: a. Fragment: catalytic protease domain. Synonym: atrolysin e. Enw. Chain: b. Engineered: yes

Source:

Protobothrops mucrosquamatus. Organism_taxid: 103944. Synthetic: yes. Other_details: the inhibitor penw was synthesized by solid-phase method.

Resolution:

1.37Å R-factor: 0.172 R-free: 0.202

Authors:

K.F.Huang,S.H.Chiou,T.P.Ko,A.H.J.Wang

Key ref:

K.F.Huang et al. (2002). Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues. Eur J Biochem, 269, 3047-3056. PubMed id: 12071970 DOI: 10.1046/j.1432-1033.2002.02982.x

Date:

22-Jan-02 Release date: 10-Jul-02

Protein chain

O57413  (VM2T3_PROMU) -  Zinc metalloproteinase/disintegrin from Protobothrops mucrosquamatus

Seq: 481 a.a.

Struc: 201 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.24.- - ?????

DOI no: 10.1046/j.1432-1033.2002.02982.x

Eur J Biochem 269:3047-3056 (2002)

PubMed id: 12071970

Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues.

K.F.Huang, S.H.Chiou, T.P.Ko, A.H.Wang.

ABSTRACT

Venoms from crotalid and viperid snakes contain several peptide inhibitors which regulate the proteolytic activities of their snake-venom metalloproteinases (SVMPs) in a reversible manner under physiological conditions. In this report, we describe the high-resolution crystal structures of a SVMP, TM-3, from Taiwan habu (Trimeresurus mucrosquamatus) cocrystallized with the endogenous inhibitors pyroGlu-Asn-Trp (pENW), pyroGlu-Gln-Trp (pEQW) or pyroGlu-Lys-Trp (pEKW). The binding of inhibitors causes some of the residues around the inhibitor-binding environment of TM-3 to slightly move away from the active-site center, and displaces two metal-coordinated water molecules by the C-terminal carboxylic group of the inhibitors. This binding adopts a retro-manner principally stabilized by four possible hydrogen bonds. The Trp indole ring of the inhibitors is stacked against the imidazole of His143 in the S-1 site of the proteinase. Results from the study of synthetic inhibitor analogues showed the primary specificity of Trp residue of the inhibitors at the P-1 site, corroborating the stacking effect observed in our structures. Furthermore, we have made a detailed comparison of our structures with the binding modes of other inhibitors including batimastat, a hydroxamate inhibitor, and a barbiturate derivative. It suggests a close correlation between the inhibitory activity of an inhibitor and its ability to fill the S-1 pocket of the proteinase. Our work may provide insights into the rational design of small molecules that bind to this class of zinc-metalloproteinases.

Selected figure(s)

Figure 3.
Fig. 3. Diagram of the active-site structure of TM-3 complexed with pENW. (A) The overall active-site structure. Proteinase molecule is represented by the solid surface-charge potential. The pENW, a cadmium ion and its ligated water molecule in the active site are denoted by a stick model and various spheres in cyan, yellow and magenta, respectively. The Cd-coordinated histidines and neighboring glutamyl residue are colored in magenta. Residues surrounding the active-site pocket are labeled. Diameters of the pocket corresponding to the S^-1 site of TM-3 are indicated in Å. (B) A skeletal representation. The active-site structure of the pENW-bound TM-3 is shown with a stick model. Residues surrounding the hydrophobic substrate binding pocket are in yellow, while those locating at bottom are in green. The possible hydrogen bonds are shown. Both figures were prepared using grasp.

Figure 5.
Fig. 5. Structural characteristics of the binding of the inhibitor P^minus;2 residues to TM-3. (A) pENW-bound TM-3. (B) pEQW-bound TM-3. (C) pEKW-bound TM-3. The proteinase and inhibitor residues are shown with a stick model, and colored in yellow and cyan, respectively. Structural water molecules related to inhibitor binding are drawn with purple spheres. The distances of possible hydrogen bonds or van der Waals contact are indicated in Å, and shown with blue dotted and red dashed lines, respectively.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2002, 269, 3047-3056) copyright 2002.

Figures were selected by the author.