PDBsum entry 1an1

Complex (serine protease/inhibitor)

PDB id: 1an1

Contents

Protein chains

223 a.a. *

40 a.a. *

Metals

_CA

Waters ×138

* Residue conservation analysis

PDB id:

1an1

Name:

Complex (serine protease/inhibitor)

Title:

Leech-derived tryptase inhibitor/trypsin complex

Structure:

Trypsin. Chain: e. Synonym: ldti. Engineered: yes. Tryptase inhibitor. Chain: i. Engineered: yes. Mutation: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421. Organ: salivary glands. Expressed in: saccharomyces cerevisiae.

Biol. unit:

Dimer (from PQS)

Resolution:

2.03Å R-factor: 0.170 R-free: 0.228

Authors:

J.P.Priestle,S.Di Marco

Key ref:

S.Di Marco and J.P.Priestle (1997). Structure of the complex of leech-derived tryptase inhibitor (LDTI) with trypsin and modeling of the LDTI-tryptase system. Structure, 5, 1465-1474. PubMed id: 9384562 DOI: 10.1016/S0969-2126(97)00296-7

Date:

26-Jun-97 Release date: 01-Jul-98

Protein chain

P00761  (TRYP_PIG) -  Trypsin from Sus scrofa

Seq: 231 a.a.

Struc: 223 a.a.*

Protein chain

P80424  (LDTI_HIRME) -  Leech-derived tryptase inhibitor C from Hirudo medicinalis

Seq: 46 a.a.

Struc: 40 a.a.

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

Enzyme reactions

• Enzyme class: Chains E, I: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1016/S0969-2126(97)00296-7

Structure 5:1465-1474 (1997)

PubMed id: 9384562

Structure of the complex of leech-derived tryptase inhibitor (LDTI) with trypsin and modeling of the LDTI-tryptase system.

S.Di Marco, J.P.Priestle.

ABSTRACT

BACKGROUND: Tryptase is a trypsin-like serine proteinase stored in the cytoplasmic granules of mast cells, which has been implicated in a number of mast cell related disorders such as asthma and rheumatoid arthritis. Unlike almost all other serine proteinases, tryptase is fully active in plasma and in the extracellular space, as there are no known natural inhibitors of tryptase in humans. Leech-derived tryptase inhibitor (LDTI), a protein of 46 amino acids, is the first molecule found to bind tightly to and specifically inhibit human tryptase in the nanomolar range. LDTI also inhibits trypsin and chymotrypsin with similar affinities. The structure of LDTI in complex with an inhibited proteinase could be used as a template for the development of low molecular weight tryptase inhibitors. RESULTS: The crystal structure of the complex between trypsin and LDTI was solved at 2.0 A resolution and a model of the LDTI-tryptase complex was created, based on this X-ray structure. LDTI has a very similar fold to the third domain of the turkey ovomucoid inhibitor. LDTI interacts with trypsin almost exclusively through its binding loop (residues 3-10) and especially through the sidechain of the specificity residue Lys8. Our modeling studies indicate that these interactions are maintained in the LDTI-tryptase complex. CONCLUSIONS: The insertion of nine residues after residue 174 in tryptase, relative to trypsin and chymotrypsin, prevents inhibition by other trypsin inhibitors and is certainly responsible for the higher specificity of tryptase relative to trypsin. In LDTI, the disulfide bond between residues 4 and 25 causes a sharp turn from the binding loop towards the N terminus, holding the N terminus away from the 174 loop of tryptase.

Selected figure(s)

Figure 6.
Figure 6. Electrostatic potential surface representation of the model of tryptase. (a) The region around the active site, including the binding loop of LDTI. (b) The same view as (a) but rotated 180°. The sidechains of the specificity residues P4 to P3' of LDTI are labeled (nomenclature of Berger and Schechter [26]), although Ala5 (P4) is hidden under the tryptase 174 insertion loop and Lys8 (P1) is buried in the S1 specificity pocket. The highly electronegative active-site area (red) corresponds well to the positively charged LDTI molecule (pI > 10). The concentrated positively charged region (blue) in tryptase, shown at the bottom of (b), could be responsible for heparin binding. (The figure was made with the program GRASP [43].)

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1465-1474) copyright 1997.

Figure was selected by the author.