PDBsum entry 1atd

Proteinase inhibitor(trypsin)

PDB id: 1atd

Contents

Protein chain

62 a.a.

References listed in PDB file

Key reference

Title

High-Resolution structure of ascaris trypsin inhibitor in solution: direct evidence for a ph-Induced conformational transition in the reactive site.

Authors

B.L.Grasberger, G.M.Clore, A.M.Gronenborn.

Ref.

Structure, 1994, 2, 669-678. [DOI no: 10.1016/S0969-2126(00)00067-8]

PubMed id

7922043

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 92%.

Abstract

BACKGROUND: The Ascaris trypsin inhibitor (ATI) is a member of a new family of serine protease inhibitors isolated from the helminthic worm Ascaris lumbricoides var suum. This family comprises five chymotrypsin/elastase inhibitors and one trypsin inhibitor. Members are characterized by the presence of five disulfide bonds (two of which are located on either side of the reactive site) in a single small protein domain of 61-62 residues. RESULTS: The solution structure of ATI has been determined at pH 2.4 and pH 4.75 by NMR spectroscopy. Iterative refinement permitted the unambiguous assignment of the pairing of the five disulfide bridges (Cys5-Cys38, Cys15-Cys33, Cys18-Cys29, Cys22-Cys60, and Cys40-Cys54) which were previously unknown. The structure includes four short beta-strands arranged in two approximately perpendicular beta-sheets. The reactive site loop is bounded by two disulfide bridges (Cys15-Cys33 and Cys18-Cys29) and is part of the long loop (residues 15-25) connecting strands beta 1 and beta 2. Comparison of the nuclear Overhauser enhancement data at the two pH values revealed significant differences centered around the reactive site. While the reactive site at pH 2.4 closely resembles that of other protease inhibitors, at pH 4.75 the reactive site loop undergoes a major conformational rearrangement involving the psi backbone torsion angles of the P2, P1 and P1' residues (residues 30-32). This is associated with a change in the positions of the side chains of Arg31 and Glu32. CONCLUSIONS: The overall three-dimensional structure of ATI posesses an unusual fold and, with the exception of the reactive site, shows no similarity to other serine protease inhibitors. The observation that the reactive site of the low pH form of ATI is similar to that of other serine proteases suggests that this is the active form of the protein.

Figure 2.
Figure 2. Stereoviews showing a superposition of all atoms (except protons and backbone carbonyl oxygen atoms) of (a) residues 16– 24, 38–40, 46–47 and 55–60 of the 32 simulated annealing structures of ATI at pH 2.4, and (b) residues 8–13, 41–47 and 55–57 of the 32 simulated annealing structures of ATI at pH 4.75. The backbone is shown in blue and the side chains in red. Figure 2. Stereoviews showing a superposition of all atoms (except protons and backbone carbonyl oxygen atoms) of (a) residues 16– 24, 38–40, 46–47 and 55–60 of the 32 simulated annealing structures of ATI at pH 2.4, and (b) residues 8–13, 41–47 and 55–57 of the 32 simulated annealing structures of ATI at pH 4.75. The backbone is shown in blue and the side chains in red.

Figure 5.
Figure 5. Ribbon diagrams of the restrained minimized mean structure of ATI at pH 2.4 shown in two approximately orthogonal views in (a) and (b). Arrows indicate the region of β-sheet (residues 11–13, 37–39, 45–49, and 53–57). The disulfide bridges are indicated by the solid lines connecting the labeled cysteine C ^α atoms. The reactive site in (a) is located in the upper right hand corner between Cys29 and Cys33, and the orientation in (a) is approximately the same as that shown in Figure 1. Figure 5. Ribbon diagrams of the restrained minimized mean structure of ATI at pH 2.4 shown in two approximately orthogonal views in (a) and (b). Arrows indicate the region of β-sheet (residues 11–13, 37–39, 45–49, and 53–57). The disulfide bridges are indicated by the solid lines connecting the labeled cysteine C ^α atoms. The reactive site in (a) is located in the upper right hand corner between Cys29 and Cys33, and the orientation in (a) is approximately the same as that shown in [4]Figure 1. (Figures generated with the program MOLSCRIPT [[5]46].)

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 669-678) copyright 1994.

Secondary reference #1

Title

Sequential resonance assignment and secondary structure determination of the ascaris trypsin inhibitor, A member of a novel class of proteinase inhibitors.

Authors

A.M.Gronenborn, M.Nilges, R.J.Peanasky, G.M.Clore.

Ref.

Biochemistry, 1990, 29, 183-189. [DOI no: 10.1021/bi00453a025]

PubMed id

2322539