Table 1.
Structures of trypsin-like proteases and zymogens in the open (E, Z) and collapsed (E*, Z*) formsa
| PDB ID | Resolution (Å) | Refs | |
|---|---|---|---|
| Collapsed form | |||
| Protease – E* | |||
| 1DST | Complement factor D mutant S215W | 2.0 | (45) |
| 1DSU, 1HFD | Complement factor D | 2.0, 2.3 | (24, 26) |
| 2XW9 | Complement factor D mutant S195A | 1.2 | (25) |
| 2XWA | Complement factor D mutant R218A | 2.8 | (25) |
| 1GVZ | Prostate specific antigen | 1.42 | (46) |
| 1LTO | αI-tryptase | 2.2 | (49) |
| 2F9Ob | αI-tryptase mutant D216G | 2.1 | (29) |
| 1RD3 | Thrombin mutant E217K | 2.5 | (42) |
| 1TQ0, 3EE0 | Thrombin mutant W215A/E217A | 2.8, 2.75 | (43, 44) |
| 2GP9, 3BEI | Thrombin mutant D102N | 1.87, 1.55 | (38, 40) |
| 3GIC | Thrombin mutant Δ146-149e | 1.55 | (37) |
| 3JZ2 | Thrombin mutant N143P | 2.4 | (39) |
| 3EDX, 3HK3, 3HK6 | Murine thrombin mutant W215A/E217A | 2.4, 1.94, 3.2 | (43) |
| 1TON | Tonin | 1.8 | (47) |
| 1YBW | Hepatocyte growth factor activator | 2.7 | (50) |
| 2B9L | Prophenoloxidase activating factor II | 2.0 | (48) |
| 3DFJ, 3E1X | Prostasin | 1.45, 1.7 | (51, 52) |
| Zymogen – Z* | |||
| 1CHG, 1EX3 | Chymotrypsinogen | 2.5, 3.0 | (53, 54) |
| 1DDJ, 1QRZ | Plasminogen | 2.0, 2.0 | (55, 56) |
| 1FDP | Profactor D | 2.1 | (23) |
| 1GVL | Prokallikrein 6 | 1.8 | (58) |
| 1MD7 | Complement profactor C1r | 3.2 | (60) |
| 1MZA, 1MZD | Progranzyme K | 2.23, 2.9 | (61) |
| 1SGF | α subunit of nerve growth factor | 3.15 | (62) |
| 3NXP | Prethrombin-1 | 2.2 | (63) |
| Open form | |||
| Protease - E | |||
| 1MD8 | Complement factor C1r | 2.8 | (60) |
| 1MH0, 1SGI | Thrombin mutant R77aA | 2.8, 2.3 | (35, 36) |
| 2PGB | Thrombin mutant C191A/C220A | 1.54 | (34) |
| 2OCV | Murine thrombin | 2.2 | (64) |
| 1NPM | Neuropsin | 2.1 | (67) |
| 2F9Ob | αI-tryptase mutant D216G | 2.1 | (29) |
| 2G51, 2G52 | Trypsin | 1.84, 1.84 | (68) |
| 2I6Q, 2I6S, 2ODP, 2ODQ | Complement factor C2a | 2.1, 2.7, 1.9, 2.3 | (65, 66) |
| Zymogen - Z | |||
| 1TGB, 1TGN | Trypsinogen | 1.8, 1.65 | (69, 70) |
| 1ZJK | Zymogen of MASP-2 | 2.18 | (72) |
| 2F83 | Coagulation factor XI | 2.87 | (73) |
| 2OK5 | Complement profactor B | 2.3 | (71) |
a
Structures of TLPs not included in the Table are in the E form but feature Ca2+ bound to regions known to affect activity and stability, and/or acetate or sulfate bound at or near the catalytic residues. Examples of such structures are β trypsin, cationic trypsin, trypsins from Fusarium oxysporum and Streptomyces gryseus and kallikrein 7. New structures of these enzymes without Ca2+ or anionic ligands near the active site will enable unambiguous assignment of the E or E* form.
b
The structure of αI-tryptase mutant D216G documents both the E and E* conformations in a 3:1 ratio (29).