PDBsum entry 1h8i

Hydrolase/hydrolase inhibitor

PDB id: 1h8i

Contents

Protein chains

253 a.a. *

27 a.a. *

Ligands

ASP-PHE-GLU-GLU-ILE-PRO-GLU-GLU-TYS-LEU

PHV

Waters ×365

* Residue conservation analysis

PDB id:

1h8i

Name:

Hydrolase/hydrolase inhibitor

Title:

X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor.

Structure:

Thrombin. Chain: h. Fragment: thrombin heavy chain. Synonym: coagulation factor ii. Hirudin i. Chain: i. Fragment: residues 55 to 64. Synonym: lepirudin. Thrombin.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421. Organism_taxid: 9606

Biol. unit:

Hexamer (from PQS)

Resolution:

1.75Å R-factor: 0.186 R-free: 0.235

Authors:

E.Skordalakes,G.G.Dodson,D.Green,J.Deadman

Key ref:

E.Skordalakes et al. (2001). Inhibition of human alpha-thrombin by a phosphonate tripeptide proceeds via a metastable pentacoordinated phosphorus intermediate. J Mol Biol, 311, 549-555. PubMed id: 11493008 DOI: 10.1006/jmbi.2001.4872

Date:

08-Feb-01 Release date: 02-Mar-01

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 253 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 27 a.a.

Enzyme reactions

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

DOI no: 10.1006/jmbi.2001.4872

J Mol Biol 311:549-555 (2001)

PubMed id: 11493008

Inhibition of human alpha-thrombin by a phosphonate tripeptide proceeds via a metastable pentacoordinated phosphorus intermediate.

E.Skordalakes, G.G.Dodson, D.S.Green, C.A.Goodwin, M.F.Scully, H.R.Hudson, V.V.Kakkar, J.J.Deadman.

ABSTRACT

X-ray crystallographic studies of human alpha-thrombin with a novel synthetic inhibitor, an acyl (alpha-aminoalkyl)phosphonate, reveal the existence of a pentacovalent phosphorus intermediate state. Crystal structures of the complex of alpha-thrombin with the phosphonate compound were determined independently using crystals of different ages. The first structure, solved from a crystal less than seven days old, showed a pentacoordinated phosphorus moiety. The second structure, determined from a crystal that was 12 weeks old, showed a tetracoordinated phosphorus moiety. In the first structure, a water molecule, made nucleophilic by coordination to His57 of alpha-thrombin, is bonded to the pentacoordinated phosphorus atom. Its position is approximately equivalent to that occupied by the water molecule responsible for hydrolytic deacylation during normal hydrolysis. The pentacoordinated phosphorus adduct collapses to give the expected pseudo tetrahedral complex, where the phosphorus atom is covalently bonded to Ser195 O(gamma). The crystallographic data presented here therefore suggest that the covalent bond formed between the inhibitor's phosphorus atom and O(gamma) of Ser195 proceeds via an addition-elimination mechanism, which involves the formation of a pentacoordinate intermediate.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the interactions of the phosphonate moiety of the tripeptide inhibitor, compound 1, at the active site of the enzyme human α-thrombin in complex I.

Figure 7.
Figure 7. The overall α-thrombin reaction mechanism based on the structures of complex I and complex II.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 549-555) copyright 2001.

Figures were selected by an automated process.