PDBsum entry 1m9u

Hydrolase

PDB id: 1m9u

Contents

Protein chains

241 a.a. *

Waters ×278

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of earthworm fibrinolytic enzyme component a: revealing the structural determinants of its dual fibrinolytic activity.

Authors

Y.Tang, D.Liang, T.Jiang, J.Zhang, L.Gui, W.Chang.

Ref.

J Mol Biol, 2002, 321, 57-68. [DOI no: 10.1016/S0022-2836(02)00559-4]

PubMed id

12139933

Abstract

Earthworm fibrinolytic enzyme component A (EFEa) from Eisenia fetida is a strong fibrinolytic enzyme that not only directly degrades fibrin, but also activates plasminogen. Proteolytic assays further revealed that it cleaved behind various P1 residue types. The crystal structure of EFEa was determined using the MIR method and refined to 2.3A resolution. The enzyme, showing the overall polypeptide fold of chymotrypsin-like serine proteases, possesses essential S1 specificity determinants characteristic of elastase. However, the beta strand at the west rim of the S1 specificity pocket is significantly elongated by a unique four-residue insertion (Ser-Ser-Gly-Leu) after Val217, which not only provides additional substrate hydrogen binding sites for distal P residues, but also causes extension of the S1 pocket at the south rim. The S2 subsite of the enzyme was partially occluded by the bulky side-chain of residue Tyr99. Structure-based inhibitor modeling demonstrated that EFEa's S1 specificity pocket was preferable for elastase-specific small hydrophobic P1 residues, while its accommodation of long and/or bulky P1 residues was also feasible if enhanced binding of the substrate and induced fit of the S1 pocket were achieved. EFEa is thereby endowed with relatively broad substrate specificity, including the dual fibrinolysis. The presence of Tyr99 at the S2 subsite indicates a preference for P2-Gly, while an induced fit of Tyr99 was also suggested for accommodation of bigger P2 residues. This structure is the first reported for an earthworm fibrinolytic enzyme component and serine protease originating from annelid worms.

Figure 3.
Figure 3. The molecular surface of EFEa with (a) electrostatic potential distribution and (b) hydrophobicity property. In (a), the regions with negative and positive charges are shown in red and blue, respectively. The S1, S2 (Tyr99) and S4 subsites are marked, as are the charged residues Asp60, Arg35 and Arg143 near the S1 pocket and residues Ser217A and Asn192 at the south border of the S1 pocket. In (b), the hydrophobic surface is shown in white, the polar surface in yellow, and the charged surface in blue (positive) and red (negative). (c) The EFEa active-site residue distribution. A sphere with 11 Å radius was drawn centered at the S1 specificity pocket. One-letter codes were used for the residues with the solvent molecules drawn as red balls and labeled with green numerals.

Figure 4.
Figure 4. Structural comparison of the active sites of EFEa and its closely related serine proteases based on their global C^a superposition. The superposition of some important active site residues is shown, including the catalytic triad and the substrate-discriminating residues (189, 226 and 216) in the S1 specificity pockets of EFEa (in yellow) and (a) tPA[50] (PDB code: 1BDA); (b) chymotrypsin (1DLK); (c) HLE (1PPG) and (d) PPE (4EST) (all in maroon). The specific inhibitors (in green) bound to the various enzymes were introduced into the active site of EFEa to demonstrate the fitting of the P1 residues. Identical residues are labeled in black, while different ones are labeled with their corresponding colors. For clarity, only the P1-P3 residues are drawn for the inhibitors.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 57-68) copyright 2002.

Secondary reference #1

Title

Crystallization and preliminary X-Ray analysis of earthworm fibrinolytic enzyme component a from eisenia fetida.

Authors

Y.Tang, J.Zhang, L.Gui, C.Wu, R.Fan, W.Chang, D.Liang.

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 1659-1661. [DOI no: 10.1107/S0907444900012907]

PubMed id

11092938

Figure 2.
Figure 2 Diffraction pattern of the EFE component A crystal. One of the half frames, with dimensions of 780 × 390 mm, is shown. The crystal-to-detector distance was 572 mm. Reflections at high resolution (about 1.7 Å) were observed at the edge of the frame.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

Pancreatic elastase

Authors

B.S.Hartley, D.M.Shotton.

Ref.

the enzymes,volume iii ...