PDBsum entry 2nqd

Hydrolase inhibitor/hydrolase

PDB id: 2nqd

Contents

Protein chains

109 a.a. *

221 a.a. *

Ligands

NAG-NAG

Metals

_NA

_CL

Waters ×564

* Residue conservation analysis

PDB id:

2nqd

Name:

Hydrolase inhibitor/hydrolase

Title:

Crystal structure of cysteine protease inhibitor, chagasin, in complex with human cathepsin l

Structure:

Chagasin. Chain: a. Synonym: cysteine protease inhibitor. Engineered: yes. Cathepsin l. Chain: b. Fragment: residues 1-220. Synonym: cysteine protease, major excreted protein, mep. Engineered: yes.

Source:

Trypanosoma cruzi. Organism_taxid: 5693. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

1.75Å R-factor: 0.150 R-free: 0.188

Authors:

I.Redzynia,G.Bujacz,A.Ljunggren,M.Jaskolski,M.Abrahamson

Key ref:

A.Ljunggren et al. (2007). Crystal structure of the parasite protease inhibitor chagasin in complex with a host target cysteine protease. J Mol Biol, 371, 137-153. PubMed id: 17561110 DOI: 10.1016/j.jmb.2007.05.005

Date:

31-Oct-06 Release date: 24-Jul-07

Protein chain

Q966X9  (CHAG_TRYCR) -  Chagasin from Trypanosoma cruzi

Seq: 110 a.a.

Struc: 109 a.a.

Protein chain

P07711  (CATL1_HUMAN) -  Procathepsin L from Homo sapiens

Seq: 333 a.a.

Struc: 221 a.a.*

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

Enzyme reactions

• Enzyme class: Chain B: E.C.3.4.22.15 - cathepsin L.
• Reaction: Specificity close to that of papain. As compared to cathepsin B, cathepsin L exhibits higher activity towards protein substrates, but has little activity on Z-Arg-Arg-NHMec, and no peptidyl-dipeptidase activity.

DOI no: 10.1016/j.jmb.2007.05.005

J Mol Biol 371:137-153 (2007)

PubMed id: 17561110

Crystal structure of the parasite protease inhibitor chagasin in complex with a host target cysteine protease.

A.Ljunggren, I.Redzynia, M.Alvarez-Fernandez, M.Abrahamson, J.S.Mort, J.C.Krupa, M.Jaskolski, G.Bujacz.

ABSTRACT

Chagasin is a protein produced by Trypanosoma cruzi, the parasite that causes Chagas' disease. This small protein belongs to a recently defined family of cysteine protease inhibitors. Although resembling well-known inhibitors like the cystatins in size (110 amino acid residues) and function (they all inhibit papain-like (C1 family) proteases), it has a unique amino acid sequence and structure. We have crystallized and solved the structure of chagasin in complex with the host cysteine protease, cathepsin L, at 1.75 A resolution. An inhibitory wedge composed of three loops (L2, L4, and L6) forms a number of contacts responsible for high-affinity binding (K(i), 39 pM) to the enzyme. All three loops interact with the catalytic groove, with the central loop L2 inserted directly into the catalytic center. Loops L4 and L6 embrace the enzyme molecule from both sides and exhibit distinctly different patterns of protein-protein recognition. Comparison with a 1.7 A structure of uncomplexed chagasin, also determined in this study, demonstrates that a conformational change of the first binding loop (L4) allows extended binding to the non-primed substrate pockets of the enzyme active site cleft, thereby providing a substantial part of the inhibitory surface. The mode of chagasin binding is generally similar, albeit distinctly different in detail, when compared to those displayed by cystatins and the cysteine protease inhibitory p41 fragment of the invariant chain. The chagasin-cathepsin L complex structure provides details of how the parasite protein inhibits a host enzyme of possible importance in host defense. The high level of structural and functional similarity between cathepsin L and the T. cruzi enzyme cruzipain gives clues to how the cysteine protease activity of the parasite can be targeted. This information will aid in the development of synthetic inhibitors for use as potential drugs for the treatment of Chagas disease.

Selected figure(s)

Figure 3.
Figure 3. Structure of the chagasin-cathepsin L complex. (a) A ribbon stereodiagram of the complex. The inhibitor molecule is colored gold and the enzyme blue. The surfaces of both proteins are marked in an analogous way. The view corresponds to the standard orientation used for cysteine proteases, along the interface between the left (L) and right (R) domains forming the sides of the active site cleft of cathepsin L. (b) Interaction of chagasin in the catalytic cleft of cathepsin L, viewed perpendicular to the standard orientation, with the L-domain behind the inhibitor molecule and the R-domain in the front. The side-chains of residues crucial for enzyme interactions are represented by sticks and balls (the disordered side-chain of K63 is shown in both alternative conformations) The enzyme is colored blue and the framework inhibitor molecule gold, with the enzyme-interacting loops L4, L2 and L6 in light yellow, orange and gold, respectively. (c)–(e) Details of the enzyme interactions of loops (c) L2, (d) L4 and (e) L6. In (c), side-chains of the interacting residues are shown in 2F[o]–F[c] electron density contoured at the 1.2ó level, to illustrate its quality.

Figure 5.
Figure 5. Superposition of chagasin with the active site of cruzipain. (a) A ribbon stereo diagram of the superposition of the chagasin–cathepsin L complex (colored as in Figure 3(a)) with cruzipain (burgundy), after least-squares fit of the C^α traces of the enzymes. The view is in the standard orientation along the active site cleft of the enzymes. (b) A detailed view of the interactions showing the central part of the chagasin inhibitory wedge (with the L4 loop light yellow and the L2 loop orange) and the complementary fragment of the L-domain of cruzipain (burgundy). The side-chains of residues crucial for the interactions are shown in ball-and-stick representation. The synthetic inhibitor P10 ([(1-(3-hydroxy-2-oxo-1-phenethyl-propylcarbamoyl)2-phenyl-ethyl]-carbamic acid pyridin-4-ylmethyl ester), from the complex with cruzipain (PDB code 1ME3) is shown in green.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 137-153) copyright 2007.

Figures were selected by an automated process.