PDBsum entry 3bef

Hydrolase

PDB id: 3bef

Contents

Protein chains

44 a.a. *

251 a.a. *

Ligands

ASN-ASP-LYS-TYR-GLU-PRO-PHE-TRP-GLU

ASP-LYS-TYR-GLU-PRO-PHE-TRP

NAG ×2

Waters ×229

* Residue conservation analysis

PDB id:

3bef

Name:

Hydrolase

Title:

Crystal structure of thrombin bound to the extracellular fragment of par1

Structure:

Prothrombin. Chain: a, d. Fragment: thrombin light chain. Synonym: coagulation factor ii. Engineered: yes. Mutation: yes. Prothrombin. Chain: b, e. Fragment: thrombin heavy chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: f2. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Gene: f2r, cf2r, par1, tr. Expression_system_taxid: 10029

Resolution:

2.20Å R-factor: 0.207 R-free: 0.248

Authors:

P.S.Gandhi,A.Bah,Z.Chen,F.S.Mathews,E.Di Cera

Key ref:

P.S.Gandhi et al. (2008). Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A, 105, 1832-1837. PubMed id: 18250335 DOI: 10.1073/pnas.0710894105

Date:

17-Nov-07 Release date: 01-Jan-08

Protein chains

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 44 a.a.

Protein chains

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 251 a.a.*

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

Enzyme reactions

• Enzyme class: Chains A, B, D, E: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

DOI no: 10.1073/pnas.0710894105

Proc Natl Acad Sci U S A 105:1832-1837 (2008)

PubMed id: 18250335

Structural identification of the pathway of long-range communication in an allosteric enzyme.

P.S.Gandhi, Z.Chen, F.S.Mathews, E.Di Cera.

ABSTRACT

Allostery is a common mechanism of regulation of enzyme activity and specificity, and its signatures are readily identified from functional studies. For many allosteric systems, structural evidence exists of long-range communication among protein domains, but rarely has this communication been traced to a detailed pathway. The thrombin mutant D102N is stabilized in a self-inhibited conformation where access to the active site is occluded by a collapse of the entire 215-219 beta-strand. Binding of a fragment of the protease activated receptor PAR1 to exosite I, 30-A away from the active site region, causes a large conformational change that corrects the position of the 215-219 beta-strand and restores access to the active site. The crystal structure of the thrombin-PAR1 complex, solved at 2.2-A resolution, reveals the details of this long-range allosteric communication in terms of a network of polar interactions.

Selected figure(s)

Figure 1.
Structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR1. (A) Thrombin is rendered in surface representation (wheat) with residues <4 Å from the bound fragment of PAR1 (stick model) colored in light blue. The orientation is centered on the 30-loop that separates exosite I on the right from the active site cleft on the left. The 60-loop occupies the upper rim of the active site. The electron density 2F[o] − F[c] map (green mesh) is contoured at 1.0σ. (B) Details of the molecular contacts at the thrombin–PAR1 interface, with hydrophobic regions of the thrombin epitope colored in orange and polar regions colored in light blue. H bonds are depicted as broken lines. Residues involved in contacts <4 Å are listed in Table 1 and are labeled in black for thrombin and red for PAR1. The extracellular fragment of PAR1 engages exosite I through polar and hydrophobic interactions.

Figure 2.
Allosteric effect induced by binding of the extracellular fragment of PAR1 (stick model in gold) to exosite I of thrombin (ribbon model in light green) on the conformation of the 215–219 β-strand and the 220-loop (blue). The position of Trp-215 and Arg-221a is indicated as a stick model. Thrombin is shown in the standard Bode orientation (29) with the active site cleft in the middle and exosite I to the right. Comparison with the free structure of thrombin (ribbon model in wheat, with the 215–219 β-strand and the 220-loop, Trp-215, and Arg-221a in red) shows a drastic rearrangement that pushes the 215–219 β-strand back >6 Å. Trp-215 and Arg-221a relocate >9 Å to restore access to the active site and primary specificity pocket that was obliterated in the free form. The allosteric communication between exosite I and the 215–219 β-strand and 220-loop spans almost 30 Å across the thrombin molecule (see also Fig. 3) and reveals a possible mechanism for the conversion of thrombin from its inactive form E* into the active form E.

Figures were selected by an automated process.