1YM0

Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin

Summary for 1YM0

• Entry DOI: 10.2210/pdb1ym0/pdb
• Descriptor: fibrinotic enzyme component B, alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: two chains, glycosylation, pyroglutamation, eight-membered ring, cis peptide bond, hydrolase
• Biological source: Eisenia fetida (common brandling worm); More
• Total number of polymer chains: 2
• Total formula weight: 29458.15

Authors

Wang, F.,Wang, C.,Li, M.,Zhang, J.P.,Gui, L.L.,An, X.M.,Chang, W.R. (deposition date: 2005-01-20, release date: 2005-04-19, Last modification date: 2024-10-16)

Primary citation

Wang, F.,Wang, C.,Li, M.,Zhang, J.P.,Gui, L.L.,An, X.M.,Chang, W.R.
Crystal structure of earthworm fibrinolytic enzyme component B: a novel, glycosylated two-chained trypsin.
J.Mol.Biol., 348:671-685, 2005

PubMed Abstract: The earthworm fibrinolytic enzyme (EFE), belonging to a group of serine proteases with strong fibrinolytic activity, has been used in a mixture as an oral drug for prevention and treatment of thrombosis in East Asia. The EFE component b (EFE-b) is one of seven EFE components from Eisenia fetida, and among them it has nearly the highest fibrinolytic activity. Here, we report its crystal structure at a resolution of 2.06A. The structural analysis shows that EFE-b should be classified as a trypsin from earthworm. However, it is distinct from other trypsins. It is a two-chained protease with an N-terminal, pyroglutamated light chain and an N-glycosylated heavy chain. Furthermore, the heavy chain contains a novel structural motif, an eight-membered ring resulting from a disulfide bridge between two neighboring cysteine residues, and a cis peptide bond exists between these two cysteine residues. The crystal structure of EFE-b provides the structural basis for its high level of stability and reveals its complicated post-translational modifications in earthworm. This structure is the first reported for a glycosylated two-chained trypsin, which may provide useful clues to explain the origin and evolution of the chymotrypsin family.

PubMed: 15826663
DOI: 10.1016/j.jmb.2005.02.055

Experimental method

X-RAY DIFFRACTION (2.06 Å)