Shift of the lid in the A2 domain. (A) Most of the differences between fV short and fV reside in the A2 domain (rmsd = 2.05 Å over 274 Cα atoms), which, in addition to the site of thrombin activation at R709 and the site of APC cleavage at R506, houses the gate (blue; 696YDYQNRL702) and the lid (orange; 672ESTVMATRKMHDRLEPEDEE691)that play an important role in the prothrombinase complex.16 In fV short, the gate shifts 18 Å at Y698 toward R709, and the lid flips almost 90° counterclockwise, with M676 and R679 moving 24 Å and 29 Å, respectively. The conformation of the gate becomes similar to that observed in fVa in the prothrombinase complex,16 with the side chains of Y696 and R701 pointing in opposite directions. The rearrangement of the lid is more drastic and exposes the acidic segment 658PDDDEDSYEIFEPP671 in a position where it could provide a locale for binding the protease domain of fXa in the conformation observed in the prothrombinase complex16 (Figure 5). This structural feature of fV short may account for its documented fVa-like activity1,5,8,9,14 and is consistent with the role of the segment 659DDDED663 in controlling the rate of cleavage of prothrombin by prothrombinase.50 The electrostatics support this conclusion because this area is in close proximity to the AR and very acidic (supplemental Figure 3). (B) The segment from 1503 to 1511 (cyan sticks) of the AR in the B domain occupies the top of the loop where the B domain changes direction (Figure 2B). The segment penetrates a crevice in the A2 domain, with the 1507EDDY1510 wedge sandwiched between residues from 505 to 516 and from 665 to 672 (green sticks). Shown are the H-bonding interactions between E1507 and R396, D1508, and R505 next to the site of APC cleavage at R506. Y1510 is in hydrophobic interaction with F668. The O atoms of S1505, S1506, and E1507 are in electrostatic clash with the side chain of E669 and may cause the segment 668FEPP671 to relocate the lid relative to its position in fV.
