PDBsum entry 1jvq

Hydrolase/hydrolase inhibitor

PDB id: 1jvq

Contents

Protein chain

406 a.a. *

Ligands

ACE-SER-GLU-ALA-ALA-ALA-SER-THR

TRP-MET-ASP-PHE-NH2

NDG ×7

NAG ×2

Waters ×44

* Residue conservation analysis

PDB id:

1jvq

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure at 2.6a of the ternary complex between antithrombin, a p14-p8 reactive loop peptide, and an exogenous tetrapeptide

Structure:

Antithrombin-iii. Chain: l, i. Synonym: antithrombin, serine (or cysteine) proteinase inhibitor, cladE C (antithrombin), member 1. P14-p8 reactive loop peptide. Chain: c. Fragment: human antithrombin p14-p8 peptide. Engineered: yes. Exogenous cholecystokinin tetrapeptide.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Other_details: plasma. Synthetic: yes. Other_details: this sequence occurs naturally in human antithrombin. Other_details: this sequence occurs naturally in cholecystokinin

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.204 R-free: 0.258

Authors:

A.Zhou,J.A.Huntington,D.A.Lomas,R.W.Carrell,P.E.Stein

Key ref:

A.Zhou et al. (2004). How small peptides block and reverse serpin polymerisation. J Mol Biol, 342, 931-941. PubMed id: 15342247 DOI: 10.1016/j.jmb.2004.07.078

Date:

31-Aug-01 Release date: 03-Jun-03

Protein chains

P01008  (ANT3_HUMAN) -  Antithrombin-III from Homo sapiens

Seq: 464 a.a.

Struc: 406 a.a.

DOI no: 10.1016/j.jmb.2004.07.078

J Mol Biol 342:931-941 (2004)

PubMed id: 15342247

How small peptides block and reverse serpin polymerisation.

A.Zhou, P.E.Stein, J.A.Huntington, P.Sivasothy, D.A.Lomas, R.W.Carrell.

ABSTRACT

Many of the late-onset dementias, including Alzheimer's disease and the prion encephalopathies, arise from the aberrant aggregation of individual proteins. The serpin family of serine protease inhibitors provides a well-defined structural example of such pathological aggregation, as its mutant variants readily form long-chain polymers, resulting in diseases ranging from thrombosis to dementia. The intermolecular linkages result from the insertion of the reactive site loop of one serpin molecule into the middle strand (s4A) position of the A beta-sheet of another molecule. We define here the structural requirements for small peptides to competitively bind to and block the s4A position to prevent this intermolecular linkage and polymerisation. The entry and anchoring of blocking-peptides is facilitated by the presence of a threonine which inserts into the site equivalent to P8 of s4A. But the critical requirement for small blocking-peptides is demonstrated in crystallographic structures of the complexes formed with selected tri- and tetrapeptides. These structures indicate that the binding is primarily due to the insertion of peptide hydrophobic side-chains into the P4 and P6 sites of s4A. The findings allow the rational design of synthetic blocking-peptides small enough to be suitable for mimetic design. This is demonstrated here with a tetrapeptide that preferentially blocks the polymerisation of a pathologically unstable serpin commonly present in people of European descent.

Selected figure(s)

Figure 1.
Figure 1. Crystal structures of serpins shown as ribbon representations. (a) The structure of antithrombin (PDB 1E05) shows the A-sheet of the serpin (red) with entry of the reactive loop (yellow) to P14. The crucial point of bifurcation of the sheet at the site of entry of P8 is circled in blue. As shown in b, A-sheet opening beyond P12 allows the insertion of the P8-P3 segment of the loop of another molecule (yellow) leading to polymer formation. Model based on the structure of a1-antichymotrypsin.28 (c) Antitrypsin can become polymerogenic through cleavage of the reactive loop as observed crystallographically.15^ and 16 The polymers are formed by sequential insertion of the C-terminal portion of the reactive loop of one molecule into the opened A-sheet of another. (d) Antithrombin is rendered polymerogenic by annealing of P14-P8/9 peptides (dark blue) to the top of the sheet, but additional annealing to P7-P4 of the peptide WMDF (light blue) blocks polymerisation.

Figure 3.
Figure 3. Stereo views of structures of the blocking peptides. (a) The lower half of the A-sheet (red) of the ternary complex of antithrombin showing the exogenous tetrapeptide WMDF (Trp-Met-Asp-Phe) in the hydrophobic enclosure formed by helix F and strands 3 and 5 of the A-sheet. Sigma a weighted 2F[0]-F[c] map contoured at one-times the rmsd of the map showing the tetrapeptide anchored by the insertion of the Met and Phe side-chains into the P6 and P4 positions of the sheet. (b) Detailed interactions of WMDF. The tetrapeptide (ball and stick) is coloured in pink and the P14-9 (ball and stick) peptide in yellow. Helix F and its connecting loop to s3A are superimposed with those of latent antithrombin (green) showing the movement of the connecting loop caused by the burial of the bulky Trp side-chain. Some of the residues (F368, I202 and I213) involved in forming hydrophobic interactions with the peptide are shown. (c) Structure of the P14-P9 antithrombin complex with the tripeptide formyl-Met-Leu-Phe binding to the lower half of the A-sheet in the P6-P4 position. The peptide forms six hydrogen bonds with adjacent main chain residues. The Met and Phe of the tripeptide with internally inserted side-chains are anchored at P6 and P4 positions, respectively, which is almost identical to the equivalent residues of the tetrapeptide WMDF. The P8 position above the peptide is occupied by a single glycerol molecule (ball and stick in green) that H-bonds to His334 in s5A, reforming the normal H-bond network of the six-stranded A-sheet formed by H334 and P8 Thr (Figure 4a). Nitrogen atoms are shown in blue, carbon atoms in black and oxygen atoms in red. Hydrogen bonds are shown as cyan broken lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 931-941) copyright 2004.

Figures were selected by an automated process.