2HNT

CRYSTALLOGRAPHIC STRUCTURE OF HUMAN GAMMA-THROMBIN

Summary for 2HNT

• Entry DOI: 10.2210/pdb2hnt/pdb
• Descriptor: GAMMA-THROMBIN, ... (5 entities in total)
• Functional Keywords: serine protease
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted, extracellular space: P00734 P00734 P00734 P00734
• Total number of polymer chains: 4
• Total formula weight: 33463.28

Authors

Tulinsky, A. (deposition date: 1994-08-23, release date: 1994-11-30, Last modification date: 2024-10-23)

Primary citation

Rydel, T.J.,Yin, M.,Padmanabhan, K.P.,Blankenship, D.T.,Cardin, A.D.,Correa, P.E.,Fenton 2nd., J.W.,Tulinsky, A.
Crystallographic structure of human gamma-thrombin.
J.Biol.Chem., 269:22000-22006, 1994

PubMed Abstract: In an effort to prepare crystals and determine the structure of alpha-thrombin complexed to a synthetic peptide inhibitor (MDL-28050) of the hirudin 54-65 COOH-terminal region, it was discovered that the crystals were not those of the complex but of gamma-thrombin. Gel electrophoresis studies revealed that autolytic degradation had occurred prior to crystallization. NH2-terminal sequence analysis of these autolytic fragments confirmed the gamma-thrombin product (cleavages at Arg75-Tyr76 and/or Arg77A-Asn78, and Lys149E-Gly150; chymotrypsinogen numbering) with a minor amount of another autolysis product, beta-thrombin (first two cleavages only). The final structure has an R-factor of 0.156 for 7.0-2.5-A data, and includes 186 water molecules. A comparison of gamma-thrombin with the thrombin structure in the alpha-thrombin-hirugen complex revealed that the two structures agreed well (r.m.s. delta = 0.39 A for main chain atoms). These structures possess uninhibited active sites where the disposition of the catalytic triad residues is nearly identical. The electron density in the vicinity of the gamma-thrombin cleavage regions is poor, and only becomes well-defined several residues prior to and after the actual cleavage sites. The extensive disorder evoked by beta-cleavage(s) in the Lys70-Glu80 loop region indicates that this part of the molecule is severely disrupted by autolysis and is the reason exosite functions are dramatically impaired in beta-and gamma-thrombin. Since autolysis did not lead to a major reorganization of the folded structure of alpha-thrombin, the likely structural features of the interaction of thrombin substrate with thrombin enzyme during beta-cleavage have been modeled by docking the exosite region of one molecule at the active site of another.

PubMed: 8071320

Experimental method

X-RAY DIFFRACTION (2.5 Å)