id: MODULE:fibrinolysis title: Fibrinolysis — plasminogen activation by tPA on fibrin and uPA/uPAR on cells, plasmin degradation of fibrin, and its serpin and TAFI brakes; PLG/PLAT/PLAU/PLAUR/SERPINE1/SERPINB2/SERPINF2/CPB2 description: >- Fibrinolysis dissolves fibrin clots. Its effector is plasmin, the active serine protease formed from the zymogen plasminogen (PLG). Plasminogen activation is catalysed by two serine proteases. Tissue-type plasminogen activator (tPA, PLAT) is a poor enzyme in solution, but on a fibrin surface it binds fibrin and then plasminogen to form a ternary complex, which lowers its Michaelis constant by orders of magnitude. This restricts plasmin formation to the clot. Fibrin is therefore both the substrate of fibrinolysis and the template for its activation step. Urokinase-type plasminogen activator (uPA, PLAU) works mainly on cell surfaces, bound to its GPI-anchored receptor uPAR (PLAUR), which focuses plasminogen activation at the pericellular surface. Plasmin cleaves fibrin into soluble degradation products. Partial digestion exposes C-terminal lysine residues that bind the kringle lysine-binding sites of plasminogen and tPA, a positive feedback that accelerates further activation. The system is held in check at three points. Plasminogen activator inhibitor-1 (PAI-1, SERPINE1) is the main fast-acting serpin inhibitor of tPA and uPA. PAI-2 (SERPINB2), protease nexin-1 (SERPINE2) and protein C inhibitor (SERPINA5) are tissue- or context-restricted plasminogen activator inhibitors. Alpha2-antiplasmin (SERPINF2) inhibits free plasmin almost instantly. Thrombin-activatable fibrinolysis inhibitor (TAFI, CPB2), once activated by the thrombin-thrombomodulin complex, is a basic carboxypeptidase that removes the C-terminal lysines from partly degraded fibrin and so removes fibrin's cofactor function. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0000481 title: fibrinolysis pathway statement: >- The module boundary and its core gene products follow the RGD interactive diagram for this Pathway Ontology term. The diagram draws the coagulation cascade pathway producing fibrin; fibrin associated with Plat and with Plg; Plat and Plau each positively affecting Plg and producing plasmin; Plau associated with Plaur; Serpine1 negatively affecting Plat and Plau; Serpinf2 negatively affecting plasmin; plasmin positively affecting fibrin (clot dissolution) and other plasmin substrates; Cpb2 acting on fibrin; and Plg associated with Plg receptors. The record text also names SERPINB2, SERPINA5 and SERPINE2 among the other serpin inhibitors. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0000481.yaml). - source_id: GO:0042730 title: fibrinolysis statement: >- The module is grounded in GO fibrinolysis, the GO mapping recorded for PW:0000481 in the project's module seeds. - source_id: GO:0031639 title: plasminogen activation statement: >- The tPA and uPA activation steps are plasminogen activation, the zymogen-activation step that produces plasmin. - source_id: PMID:7199524 title: Kinetics of the activation of plasminogen by human tissue plasminogen activator. Role of fibrin. statement: >- Establishes fibrin as the template on which tPA activates plasminogen through an ordered ternary complex, confining plasmin formation to the clot. supporting_text: The Low Michaelis constant in the presence of fibrin allows efficient plasminogen activation on a fibrin clot, while its high value in the absence of fibrin prevents efficient activation in plasma. - source_id: PMID:8133887 title: Physiological consequences of loss of plasminogen activator gene function in mice. statement: >- Genetic evidence that tPA and uPA are the two physiological plasminogen activators of fibrinolysis, with partly redundant roles. supporting_text: Inactivation of the t-PA gene impairs clot lysis and inactivation of the u-PA gene results in occasional fibrin deposition. Mice with combined t-PA and u-PA deficiency suffer extensive spontaneous fibrin deposition - source_id: PMID:7705657 title: Plasminogen deficiency causes severe thrombosis but is compatible with development and reproduction. statement: >- Genetic evidence that plasminogen is the central effector of fibrinolysis. supporting_text: Plg plays a pivotal role in fibrinolysis and hemostasis - source_id: PMID:9765237 title: A study of the mechanism of inhibition of fibrinolysis by activated thrombin-activable fibrinolysis inhibitor. statement: >- Defines the lysine-dependent positive feedback of partly degraded fibrin and the mechanism by which activated TAFI removes it. supporting_text: We conclude that TAFIa suppresses fibrinolysis by removing COOH-terminal lysine and arginine residues from fibrin, thereby reducing its cofactor functions in both plasminogen activation and the positive feedback conversion of Glu-plasminogen to Lys-plasminogen. notes: >- Derived from the RGD Pathway Ontology diagram PW:0000481 through the RGD_PATHWAY_ONTOLOGY project's diagram->module route. The RGD diagram supplied the boundary, the seven drawn gene products (Plg, Plat, Plau, Plaur, Serpine1, Serpinf2, Cpb2) and the topology; fibrinogen (FGA, FGB, FGG, drawn as the "fibrin" node) and the serpins the record names in prose (SERPINB2, SERPINE2, SERPINA5) were added as participants. Activation, effector and inhibition are separate parts. Molecular functions were chosen from each protein's experimental GO annotations in QuickGO: PLAT, PLAU and PLG serine-type endopeptidase activity GO:0004252 (IDA; PLG also EXP); PLAUR enzyme activator activity GO:0008047 (IDA, PMID:1689240), chosen over urokinase plasminogen activator receptor activity GO:0030377 (also IDA), because GO:0030377 is defined as initiating a change in cell activity, which is signalling and not the localisation and acceleration of plasminogen activation that this module needs; SERPINE1, SERPINF2, SERPINE2 and SERPINA5 serine-type endopeptidase inhibitor activity GO:0004867 (IDA); SERPINB2 GO:0004867 (IBA and TAS only in GOA; its urokinase inhibition is shown in PMID:3029122); CPB2 metallocarboxypeptidase activity GO:0004181 (TAS and IBA only in GOA; the activity is shown in PMID:7782309 and PMID:9765237). Fibrin's template role was the hardest call. Fibrinogen's own experimental molecular functions are structural molecule activity GO:0005198 (IDA) and contributes_to signaling receptor binding GO:0005102, neither of which is the acceleration of tPA-mediated plasminogen activation, and the generic protein-macromolecule adaptor activity GO:0030674 on FGA is IBA only. No GO molecular function states "cofactor for plasminogen activation", so the fibrin annoton carries no function term; its role is described in prose and carried by its experimental process annotations plasminogen activation GO:0031639 and fibrinolysis GO:0042730 (IDA, PMID:16846481). Fibrinogen is kept as a participant rather than excluded because, as the repository guidance sets out with fibrinolysis as its worked example, fibrin does part of the work: it polymerises and then acts as the template that lowers the Michaelis constant for tPA-mediated plasminogen activation (PMID:7199524) and, once partly degraded, supplies the C-terminal lysines that drive the positive feedback whose removal by TAFIa suppresses lysis (PMID:9765237). Fibrin clot formation itself (thrombin, factor XIII) is out of scope and belongs to modules/coagulation_cascade.yaml; fibrin is this module's input, which the RGD diagram draws as an edge from the coagulation cascade pathway (PW:0000474). Contact-pathway/kallikrein activation of pro-uPA is likewise out of scope and belongs to modules/kallikrein_kinin_cascade.yaml. Extracellular-matrix roles of plasmin are out of scope; the one human GO-CAM that covers these proteins, gomodel:68fac5ed00001527 "Plasminogen/plasmin function in extracellular matrix disassembly", models PLAUR enzyme activator activity, PLAU and PLG serine-type endopeptidase activity in that ECM context, and its PLAU, PLAUR and PLG activities are linked here under gocam_associations because the gene and molecular function match even though the model's process is extracellular matrix disassembly rather than fibrinolysis. No GO-CAM covers the tPA, serpin or TAFI steps, and there are no gene reviews for any of the thirteen gene products, so every molecular function here was taken from QuickGO and the primary literature directly. All cited publications are abstract-only in the publications cache. module: id: fibrinolysis label: Fibrinolysis module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: fibrinolysis term: id: GO:0042730 label: fibrinolysis description: >- Solubilisation of fibrin by plasmin, with plasmin generated from plasminogen on the fibrin surface by tPA and on cell surfaces by uPA/uPAR, and restrained by serpins and by TAFI-mediated removal of fibrin's C-terminal lysines. context: cellular_components: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region - preferred_term: cell surface term: id: GO:0009986 label: cell surface description: >- Asserted in addition to the extracellular region because the uPA/uPAR arm of plasminogen activation is specifically pericellular rather than fluid-phase. parts: - order: 1 role: fibrin-templated plasminogen activation by tPA node: id: fibrinolysis_tpa_activation label: tPA activation of plasminogen on the fibrin surface module_type: REACTION description: >- tPA binds fibrin through its finger and kringle-2 domains and then binds plasminogen, forming a ternary complex on the clot. The assembled complex activates plasminogen with a Michaelis constant orders of magnitude lower than tPA achieves in solution, so plasmin is generated on the clot and not in plasma. annotons: - id: plat_plasminogen_activation label: tPA (PLAT) plasminogen activator activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PLAT (tPA) term: id: UniProtKB:P00750 label: Tissue-type plasminogen activator function: preferred_term: serine-type endopeptidase activity term: id: GO:0004252 label: serine-type endopeptidase activity substrates: - preferred_term: plasminogen term: id: UniProtKB:P00747 label: Plasminogen processes: - preferred_term: plasminogen activation term: id: GO:0031639 label: plasminogen activation locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Cleaves the Arg-Val activation bond of plasminogen to generate plasmin; intrinsically a poor enzyme that becomes efficient when co-localised with plasminogen on fibrin. evidence: - source_id: PMID:7199524 statement: >- Fibrin binds tPA and then plasminogen, giving an ordered ternary complex on the clot surface. supporting_text: The kinetic analysis suggested that the activation in the presence of fibrin occurs through binding of an activator molecule to the clot surface and subsequent addition of plasminogen (sequential ordered mechanism) to form a cyclic ternary complex. - source_id: PMID:8133887 statement: Loss of tPA in mice impairs clot lysis. supporting_text: Inactivation of the t-PA gene impairs clot lysis and inactivation of the u-PA gene results in occasional fibrin deposition. - id: fibrin_activation_template label: Fibrin as template and cofactor for tPA-mediated plasminogen activation participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: fibrin(ogen) (FGA/FGB/FGG) term: id: GO:0005577 label: fibrinogen complex description: >- The three fibrinogen chains, polymerised into fibrin by the coagulation cascade, which this module takes as its input. active_units: - id: fga_unit label: fibrinogen alpha chain role: >- Carries the alpha-chain C-terminal region; its Aalpha R16C variant makes clots fibrinolysis-resistant. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: FGA term: id: UniProtKB:P02671 label: Fibrinogen alpha chain - id: fgb_unit label: fibrinogen beta chain role: Structural chain of the fibrin polymer. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: FGB term: id: UniProtKB:P02675 label: Fibrinogen beta chain - id: fgg_unit label: fibrinogen gamma chain role: Structural chain of the fibrin polymer. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: FGG term: id: UniProtKB:P02679 label: Fibrinogen gamma chain processes: - preferred_term: plasminogen activation term: id: GO:0031639 label: plasminogen activation - preferred_term: fibrinolysis term: id: GO:0042730 label: fibrinolysis locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Fibrin is not a passive substrate here. It provides adjacent binding sites for tPA and plasminogen, positioning the pair so that activation proceeds with a low Michaelis constant, and after partial plasmin digestion it exposes C-terminal lysines that bind plasminogen and tPA kringle domains and accelerate further activation. No GO molecular function expresses this cofactor role, so none is asserted; see the module notes. evidence: - source_id: PMID:7199524 statement: >- Fibrin confines efficient plasminogen activation to the clot; without it the Michaelis constant is too high for activation in plasma. supporting_text: The Low Michaelis constant in the presence of fibrin allows efficient plasminogen activation on a fibrin clot, while its high value in the absence of fibrin prevents efficient activation in plasma. - source_id: PMID:16846481 statement: >- A fibrinogen Aalpha chain mutation makes the clot resistant to fibrinolysis without reducing plasmin generation; this is the IDA source for the fibrinogen chains' plasminogen activation and fibrinolysis annotations. supporting_text: This report characterises the defect in fibrinolysis seen as a result of the Aalpha R16C mutation. - source_id: PMID:9765237 statement: >- Plasmin-modified fibrin raises the rate constant for plasminogen activation 2.5-fold, the cofactor function TAFIa removes. supporting_text: TAFIa prevents a 2.5-fold increase in the rate constant for plasminogen activation which occurs when fibrin is modified by plasmin in the early course of fibrin degradation. - order: 2 role: receptor-focused plasminogen activation by uPA node: id: fibrinolysis_upa_activation label: uPA/uPAR activation of plasminogen at the cell surface module_type: REACTION description: >- uPA bound to its GPI-anchored receptor uPAR is held at the plasma membrane, which focuses plasminogen activation at the pericellular surface rather than on fibrin. annotons: - id: plau_plasminogen_activation label: uPA (PLAU) plasminogen activator activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PLAU (uPA) term: id: UniProtKB:P00749 label: Urokinase-type plasminogen activator function: preferred_term: serine-type endopeptidase activity term: id: GO:0004252 label: serine-type endopeptidase activity substrates: - preferred_term: plasminogen term: id: UniProtKB:P00747 label: Plasminogen processes: - preferred_term: plasminogen activation term: id: GO:0031639 label: plasminogen activation locations: - preferred_term: cell surface term: id: GO:0009986 label: cell surface role_description: >- Second physiological plasminogen activator; acts mainly receptor-bound at the cell surface, so its contribution to clot lysis is cell-associated. evidence: - source_id: PMID:1689240 statement: >- Receptor-bound uPA activates plasminogen at the cell surface. supporting_text: the transfected mouse LB6 cells specifically bind human uPA, which in turn activates plasminogen - source_id: PMID:8133887 statement: >- uPA loss alone gives occasional fibrin deposition; combined tPA and uPA loss gives extensive spontaneous fibrin deposition. supporting_text: Mice with combined t-PA and u-PA deficiency suffer extensive spontaneous fibrin deposition, with its associated effects on growth, fertility and survival. gocam_associations: - model: gomodel:68fac5ed00001527 activity: gomodel:68fac5ed00001527/68fac5ed00001540 title: PLAU serine-type endopeptidase activity (GO:0004252) at the cell surface description: >- Same gene and molecular function as this annoton; in that model the activity is placed in positive regulation of extracellular matrix disassembly rather than fibrinolysis. - id: plaur_focusing label: uPAR (PLAUR) localisation and activation of uPA participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PLAUR (uPAR) term: id: UniProtKB:Q03405 label: Urokinase plasminogen activator surface receptor function: preferred_term: enzyme activator activity term: id: GO:0008047 label: enzyme activator activity targets: - preferred_term: PLAU (uPA) term: id: UniProtKB:P00749 label: Urokinase-type plasminogen activator processes: - preferred_term: plasminogen activation term: id: GO:0031639 label: plasminogen activation locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Binds uPA and holds it on the membrane, concentrating plasminogen activation at the cell surface. The alternative term urokinase plasminogen activator receptor activity (GO:0030377) is defined as initiating a change in cell activity, i.e. signalling, which is not the role modelled here. evidence: - source_id: PMID:1689240 statement: >- uPAR regulates plasminogen-mediated extracellular proteolysis from the cell surface. supporting_text: The surface receptor for urokinase plasminogen activator (uPAR) has been recognized in recent years as a key molecule in regulating plasminogen mediated extracellular proteolysis. gocam_associations: - model: gomodel:68fac5ed00001527 activity: gomodel:68fac5ed00001527/68fac5ed00001533 title: PLAUR enzyme activator activity (GO:0008047) at the plasma membrane description: >- Same gene and molecular function as this annoton, upstream of the PLAU activity in that model. - order: 3 role: plasmin degradation of fibrin node: id: fibrinolysis_plasmin_effector label: Plasmin degradation of fibrin module_type: REACTION description: >- Plasmin, the active two-chain protease derived from plasminogen, cleaves fibrin into soluble degradation products, dissolving the clot. annotons: - id: plg_plasmin_activity label: Plasmin (PLG) fibrinolytic protease activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PLG (plasminogen/plasmin) term: id: UniProtKB:P00747 label: Plasminogen function: preferred_term: serine-type endopeptidase activity term: id: GO:0004252 label: serine-type endopeptidase activity substrates: - preferred_term: fibrinogen alpha chain (fibrin) term: id: UniProtKB:P02671 label: Fibrinogen alpha chain - preferred_term: fibrinogen beta chain (fibrin) term: id: UniProtKB:P02675 label: Fibrinogen beta chain - preferred_term: fibrinogen gamma chain (fibrin) term: id: UniProtKB:P02679 label: Fibrinogen gamma chain processes: - preferred_term: fibrinolysis term: id: GO:0042730 label: fibrinolysis locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- The effector of the module: the zymogen circulates, and the plasmin formed from it on the clot cleaves fibrin. Partial digestion also exposes the C-terminal lysines that feed back on activation (part 1). evidence: - source_id: PMID:7705657 statement: >- Plasminogen-null mice develop widespread fibrin deposition and thrombosis, establishing plasmin as the fibrinolytic effector. supporting_text: Plg plays a pivotal role in fibrinolysis and hemostasis - source_id: PMID:9765237 statement: >- Fibrinolysis can be driven directly by plasmin, which TAFIa inhibits at elevated concentrations. supporting_text: TAFIa also inhibits plasmin activity in a clot and prolongs fibrinolysis initiated with plasmin. gocam_associations: - model: gomodel:68fac5ed00001527 activity: gomodel:68fac5ed00001527/68fac5ed00001547 title: PLG serine-type endopeptidase activity (GO:0004252) in the extracellular region description: >- Same gene and molecular function as this annoton; that model places the activity in extracellular matrix disassembly, downstream of uPA, rather than in fibrinolysis. - order: 4 role: serpin inhibition of the plasminogen activators node: id: fibrinolysis_activator_inhibition label: Serpin inhibition of tPA and uPA module_type: REGULATORY_STEP description: >- Serpins form irreversible covalent complexes with the plasminogen activators, which can no longer activate plasminogen. PAI-1 is the principal fast circulating inhibitor; PAI-2, protease nexin-1 and protein C inhibitor act in restricted tissue or cellular settings. annotons: - id: serpine1_pai1 label: PAI-1 (SERPINE1) inhibition of tPA and uPA participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SERPINE1 (PAI-1) term: id: UniProtKB:P05121 label: Plasminogen activator inhibitor 1 function: preferred_term: serine-type endopeptidase inhibitor activity term: id: GO:0004867 label: serine-type endopeptidase inhibitor activity targets: - preferred_term: PLAT (tPA) term: id: UniProtKB:P00750 label: Tissue-type plasminogen activator - preferred_term: PLAU (uPA) term: id: UniProtKB:P00749 label: Urokinase-type plasminogen activator processes: - preferred_term: negative regulation of plasminogen activation term: id: GO:0010757 label: negative regulation of plasminogen activation - preferred_term: negative regulation of fibrinolysis term: id: GO:0051918 label: negative regulation of fibrinolysis locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Main physiological brake on plasminogen activation; also active while bound to fibrin within the thrombus. evidence: - source_id: PMID:2503541 statement: >- Fibrin-bound activated PAI-1 complexes both activators and abolishes their ability to activate plasminogen. supporting_text: This reactive site of activated PAI-1 bound to fibrin is fully exposed to form complexes with t-PA and u-PA, that are unable to activate plasminogen. - source_id: PMID:8254029 statement: >- PAI-1-deficient mice are mildly hyperfibrinolytic, confirming PAI-1 as a physiological brake rather than an essential component. supporting_text: disruption of the PAI-1 gene in mice appears to induce a mild hyperfibrinolytic state and a greater resistance to venous thrombosis but not to impair hemostasis - id: serpinb2_pai2 label: PAI-2 (SERPINB2) inhibition of uPA participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SERPINB2 (PAI-2) term: id: UniProtKB:P05120 label: Plasminogen activator inhibitor 2 function: preferred_term: serine-type endopeptidase inhibitor activity term: id: GO:0004867 label: serine-type endopeptidase inhibitor activity targets: - preferred_term: PLAU (uPA) term: id: UniProtKB:P00749 label: Urokinase-type plasminogen activator role_description: >- Ov-serpin of monocytes and placenta, selective for uPA; mostly intracellular with a secreted fraction, so its contribution is restricted rather than systemic. No experimental fibrinolysis process annotation exists for it in GOA, so none is asserted here. evidence: - source_id: PMID:3029122 statement: >- Recombinant placental PAI-2 inhibits urokinase and forms a covalent complex with it. supporting_text: The expressed protein inhibited the activity of human urokinase in a fibrin autography assay, and formed a 79-kDa (reduced) covalent complex with 125I-urokinase that could be immunoprecipitated with anti-PAI. - source_id: PMID:3029122 statement: PAI-2 is a serpin distinct from endothelial PAI-1. supporting_text: Thus placental PAI is a unique member of the serpin gene family, distinct from endothelial-type PAI. - id: serpine2_pn1 label: Protease nexin-1 (SERPINE2) inhibition of uPA participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SERPINE2 (protease nexin-1) term: id: UniProtKB:P07093 label: Glia-derived nexin function: preferred_term: serine-type endopeptidase inhibitor activity term: id: GO:0004867 label: serine-type endopeptidase inhibitor activity targets: - preferred_term: PLAU (uPA) term: id: UniProtKB:P00749 label: Urokinase-type plasminogen activator processes: - preferred_term: negative regulation of plasminogen activation term: id: GO:0010757 label: negative regulation of plasminogen activation locations: - preferred_term: cell surface term: id: GO:0009986 label: cell surface role_description: >- Platelet-derived serpin, barely detectable in plasma, that inhibits uPA (and thrombin) at the platelet surface; included because platelet PN-1 has direct functional and knockout evidence, in line with the "only with evidence" boundary for this serpin. evidence: - source_id: PMID:19855083 statement: PN-1 inhibits plasminogen activators and plasmin. supporting_text: Protease nexin-1 (PN-1) is a serpin that inhibits plasminogen activators, plasmin, and thrombin. - source_id: PMID:19855083 statement: >- Antibody blockade and mouse knockout both show platelet PN-1 acts on uPA; this is the IMP source for its negative regulation of plasminogen activation annotation. supporting_text: Both approaches indicate that platelet PN-1 is active on thrombin and urokinase-type plasminogen activator. - id: serpina5_pci label: Protein C inhibitor (SERPINA5) inhibition of uPA participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SERPINA5 (protein C inhibitor, PAI-3) term: id: UniProtKB:P05154 label: Plasma serine protease inhibitor function: preferred_term: serine-type endopeptidase inhibitor activity term: id: GO:0004867 label: serine-type endopeptidase inhibitor activity targets: - preferred_term: PLAU (uPA) term: id: UniProtKB:P00749 label: Urokinase-type plasminogen activator locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Heparin-accelerated plasma serpin, historically PAI-3, included on the strength of direct kinetic evidence of urokinase inhibition. It has no fibrinolysis-related process annotation in GOA and is a broad-spectrum inhibitor, so its weight in fibrinolysis is minor. evidence: - source_id: PMID:3501295 statement: >- Purified protein C inhibitor inhibits urokinase and is identical to PAI-3. supporting_text: PCI revealed itself as a non-competitive inhibitor of u-PA. - source_id: PMID:3501295 statement: Inhibition proceeds through a 1:1 covalent complex with uPA. supporting_text: Inhibition of amidolytic activity was found to be associated with the formation of an 1:1 equimolar complex with a Mr of 110,000 - order: 5 role: alpha2-antiplasmin inhibition of plasmin node: id: fibrinolysis_plasmin_inhibition label: Alpha2-antiplasmin inhibition of plasmin module_type: REGULATORY_STEP description: >- Alpha2-antiplasmin inhibits free plasmin almost instantaneously, confining plasmin activity to the clot where it is protected by fibrin binding. annotons: - id: serpinf2_a2ap label: Alpha2-antiplasmin (SERPINF2) inhibition of plasmin participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SERPINF2 (alpha-2-antiplasmin) term: id: UniProtKB:P08697 label: Alpha-2-antiplasmin function: preferred_term: serine-type endopeptidase inhibitor activity term: id: GO:0004867 label: serine-type endopeptidase inhibitor activity targets: - preferred_term: plasmin (PLG) term: id: UniProtKB:P00747 label: Plasminogen processes: - preferred_term: negative regulation of fibrinolysis term: id: GO:0051918 label: negative regulation of fibrinolysis locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Acts on the effector rather than the activators, at close to the diffusion limit, and accounts for essentially all plasma antiplasmin activity against activator-induced clot lysis. evidence: - source_id: PMID:134998 statement: >- Alpha2-plasmin inhibitor was isolated as the plasma protein that blocks activator-induced fibrin clot lysis. supporting_text: A procedure is presented for purifying a novel proteinase inhibitor in human plasma whose apparent unique biological property is to inhibit efficiently the lysis of fibrin clots induced by plasminogen activator. - source_id: PMID:134998 statement: >- Inhibition is near-instantaneous on plasmin, not on the activator, so it acts at the effector step. supporting_text: Inhibition of plasmin by the inhibitor is almost instantaneous even at 0 degrees, in contrast to the slow inhibition of urokinase (plasminogen activator in urine). - order: 6 role: TAFI removal of fibrin C-terminal lysines node: id: fibrinolysis_tafi_lysine_removal label: TAFIa (CPB2) removal of C-terminal lysines from partly degraded fibrin module_type: REGULATORY_STEP description: >- Thrombin bound to thrombomodulin cleaves TAFI to TAFIa, a basic carboxypeptidase that excises the C-terminal lysine and arginine residues plasmin exposes on fibrin, withdrawing fibrin's cofactor function and slowing lysis. The thrombin-thrombomodulin activation step itself belongs to the coagulation module. annotons: - id: cpb2_tafia label: TAFIa (CPB2) carboxypeptidase activity on fibrin participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CPB2 (TAFI) term: id: UniProtKB:Q96IY4 label: Carboxypeptidase B2 function: preferred_term: metallocarboxypeptidase activity term: id: GO:0004181 label: metallocarboxypeptidase activity substrates: - preferred_term: plasmin-modified fibrin alpha chain term: id: UniProtKB:P02671 label: Fibrinogen alpha chain - preferred_term: plasmin-modified fibrin beta chain term: id: UniProtKB:P02675 label: Fibrinogen beta chain - preferred_term: plasmin-modified fibrin gamma chain term: id: UniProtKB:P02679 label: Fibrinogen gamma chain processes: - preferred_term: negative regulation of fibrinolysis term: id: GO:0051918 label: negative regulation of fibrinolysis - preferred_term: negative regulation of plasminogen activation term: id: GO:0010757 label: negative regulation of plasminogen activation locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- The only non-serpin brake in the module, and the only one that works by modifying the substrate rather than inhibiting an enzyme: it strips the lysines that make partly degraded fibrin a better cofactor. evidence: - source_id: PMID:7782309 statement: >- TAFI was purified as the thrombin-activated plasma protein that retards tPA-induced clot lysis, and is a carboxypeptidase B precursor. supporting_text: Amino-terminal sequence analyses identified TAFI as a precursor of a plasma carboxypeptidase B (CPB). - source_id: PMID:7782309 statement: Activated TAFI blocks activation of Glu-plasminogen. supporting_text: Activated TAFI inhibits the activation of Glu-plasminogen but does not prolong the lysis of clots formed in the presence of Lys-plasminogen. - source_id: PMID:9765237 statement: >- The mechanism is removal of C-terminal lysine and arginine residues from fibrin, abolishing its cofactor functions. supporting_text: We conclude that TAFIa suppresses fibrinolysis by removing COOH-terminal lysine and arginine residues from fibrin, thereby reducing its cofactor functions in both plasminogen activation and the positive feedback conversion of Glu-plasminogen to Lys-plasminogen. connections: - source: fibrinolysis_tpa_activation target: fibrinolysis_plasmin_effector connection_type: PROVIDES_INPUT_FOR description: >- tPA acting on fibrin-bound plasminogen generates the plasmin that degrades the clot. - source: fibrinolysis_upa_activation target: fibrinolysis_plasmin_effector connection_type: PROVIDES_INPUT_FOR description: >- Receptor-bound uPA generates plasmin at the cell surface, the second route into the effector step. - source: fibrinolysis_plasmin_effector target: fibrinolysis_tpa_activation connection_type: POSITIVELY_REGULATES description: >- Plasmin-modified fibrin exposes C-terminal lysines that bind plasminogen and tPA kringles and raise the rate constant for activation, a positive feedback loop (PMID:9765237). - source: fibrinolysis_activator_inhibition target: fibrinolysis_tpa_activation connection_type: NEGATIVELY_REGULATES description: PAI-1 complexes tPA, in plasma and on fibrin, blocking activation. - source: fibrinolysis_activator_inhibition target: fibrinolysis_upa_activation connection_type: NEGATIVELY_REGULATES description: >- PAI-1, PAI-2, protease nexin-1 and protein C inhibitor all inhibit uPA, the receptor-bound arm. - source: fibrinolysis_plasmin_inhibition target: fibrinolysis_plasmin_effector connection_type: NEGATIVELY_REGULATES description: >- Alpha2-antiplasmin inactivates plasmin that escapes the clot, and in excess also plasmin within it. - source: fibrinolysis_tafi_lysine_removal target: fibrinolysis_tpa_activation connection_type: NEGATIVELY_REGULATES description: >- TAFIa removes the C-terminal lysines on which the positive feedback into tPA- mediated activation depends. - source: fibrinolysis_tafi_lysine_removal target: fibrinolysis_plasmin_effector connection_type: NEGATIVELY_REGULATES description: >- At elevated concentrations TAFIa also directly inhibits plasmin activity within the clot (PMID:9765237).