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TitleProthrombinase processivity is conferred by substrate allostery.
Journal, issue, pagesEMBO J, Vol. 45, Issue 11, Page 3954-3977, Year 2026
Publish dateApr 22, 2026
AuthorsFatma Işık Üstok / Alexandre Faille / Alan J Warren / James A Huntington /
PubMed AbstractThe prothrombinase complex, comprised of factor (f) Xa and fVa, converts prothrombin to thrombin through sequential cleavage at two sites in a rapid and processive manner. The molecular basis of ...The prothrombinase complex, comprised of factor (f) Xa and fVa, converts prothrombin to thrombin through sequential cleavage at two sites in a rapid and processive manner. The molecular basis of prothrombin processing is an enzymatical mystery that to solve requires structural insight into how the substrate and intermediate bind to prothrombinase. Here we present two 3.1 Å cryo-EM structures of prothrombinase bound to prothrombin and to meizothrombin. The prothrombin complex revealed a surprising interaction between the end of the heavy chain of fVa with exosite I of prothrombin, accounting for 70% of the contact interface. Triggering of the zymogen-to-protease conformational change following cleavage at Arg320 alters all domain-domain and fVa interactions observed for prothrombin, and results in a large-scale rearrangement of meizothrombin that presents the second cleavage site (Arg271) for processing. Together, these structures reveal a remarkable enzymatic mechanism that requires the active participation of the substrate itself, and introduces a new paradigm of 'substrate allostery'.
External linksEMBO J / PubMed:42020574 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.8 - 3.1 Å
Structure data

56052

9tle

EMDB-56052, PDB-9tle:
Structure of human prothrombinase with prothrombin
Method: EM (single particle) / Resolution: 3.1 Å

56054

9tlg

EMDB-56054, PDB-9tlg:
Structure of human prothrombinase with meizothrombin
Method: EM (single particle) / Resolution: 3.1 Å

PDB-9t00:
Crystal structure of prethrombin-2 with a peptide corresponding to the C-terminus of the heavy chain of factor Va
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-CA:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • homo sapiens (human)
KeywordsBLOOD CLOTTING / enzyme / zymogen / complex / prothrombinase / factor Va / factor Xa / prothrombin / meizothrombin

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