PDBsum entry 1oph

Hydrolase/hydrolase inhibitor

PDB id: 1oph

Contents

Protein chains

375 a.a. *

223 a.a. *

Waters ×377

* Residue conservation analysis

PDB id:

1oph

Name:

Hydrolase/hydrolase inhibitor

Title:

Non-covalent complex between alpha-1-pi-pittsburgh and s195a trypsin

Structure:

Alpha-1-antitrypsin precursor. Chain: a. Fragment: alpha-1-antitrypsin (residues 26-418). Synonym: alpha-1 protease inhibitor, alpha-1- antiproteinase, pro0684/pro2209. Engineered: yes. Mutation: yes. Trypsinogen, cationic precursor. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Gene: serpina1 or pi or aat. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: sg13009. Bos taurus.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.190 R-free: 0.229

Authors:

A.Dementiev,M.Simonovic,K.Volz,P.G.Gettins

Key ref:

A.Dementiev et al. (2003). Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases. J Biol Chem, 278, 37881-37887. PubMed id: 12860985 DOI: 10.1074/jbc.M305195200

Date:

05-Mar-03 Release date: 05-Aug-03

Protein chain

P01009  (A1AT_HUMAN) -  Alpha-1-antitrypsin from Homo sapiens

Seq: 418 a.a.

Struc: 375 a.a.*

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Enzyme reactions

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

DOI no: 10.1074/jbc.M305195200

J Biol Chem 278:37881-37887 (2003)

PubMed id: 12860985

Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases.

A.Dementiev, M.Simonovic, K.Volz, P.G.Gettins.

ABSTRACT

The serpin antithrombin is a slow thrombin inhibitor that requires heparin to enhance its reaction rate. In contrast, alpha1-proteinase inhibitor (alpha1PI) Pittsburgh (P1 Met --> Arg natural variant) inhibits thrombin 17 times faster than pentasaccharide heparin-activated antithrombin. We present here x-ray structures of free and S195A trypsin-bound alpha1PI Pittsburgh, which show that the reactive center loop (RCL) possesses a canonical conformation in the free serpin that does not change upon binding to S195A trypsin and that contacts the proteinase only between P2 and P2'. By inference from the structure of heparin cofactor II bound to S195A thrombin, this RCL conformation is also appropriate for binding to thrombin. Reaction rates of trypsin and thrombin with alpha1PI Pittsburgh and antithrombin and their P2 variants show that the low antithrombin-thrombin reaction rate results from the antithrombin RCL sequence at P2 and implies that, in solution, the antithrombin RCL must be in a similar canonical conformation to that found here for alpha1PI Pittsburgh, even in the nonheparin-activated state. This suggests a general, limited, canonical-like interaction between serpins and proteinases in their Michaelis complexes.

Selected figure(s)

Figure 4.
FIG. 4. Thrombin and its interactions with inhibitors. a, superposition, in stereo, of thrombin or S195A thrombin structures of complexes with PPACK (gold) (Protein Data Bank code 1HAI [PDB] ), with BPTI (green) (Protein Data Bank code 1BTH [PDB] ), and with heparin cofactor II (red) (Protein Data Bank code 1JMO [PDB] ), showing the identical conformations of all regions except the surface loops flanking the active site, particularly the 60 loop and 150 loop. b, stereo representation of the P5-P5' residues of [1]PI Pittsburgh (cyan) from the noncovalent complex with S195A trypsin docked into the thrombin structure found in the noncovalent complex of S195A thrombin with heparin cofactor II (HCII in magenta).

Figure 5.
FIG. 5. Antithrombin RCL conformation and modeled interaction with thrombin. a, superposition, in stereo, of the conformations of P5-P5' residues of [1]PI Pittsburgh from its noncovalent complex with S195A trypsin and of pentasacharide-activated antithrombin from a structure of the heterodimer (orange) (Protein Data Bank code 1AZX [PDB] ). These RCLs are aligned such that the P1 residues have the same horizontal position. The view is rotated 90° anticlockwise relative to Fig. 1b. b, stereo representation of the P5-P5' residues of antithrombin from the x-ray structure of antithrombin heterodimer docked into the thrombin structure found in the noncovalent complex of S195A thrombin with heparin cofactor II, showing inappropriate positioning relative to the catalytic triad and unfavorable interactions with surface loops.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 37881-37887) copyright 2003.

Figures were selected by an automated process.