matrixdb Institut de Biologie et de Chimie des Prot\u00c3\u00a9ines, 7, passage du Vercors 69 367 Lyon cedex 07 FRANCE matrixdb@ibcp.fr http://matrixdb.ibcp.fr Mock publication and experiment for abstract interactions that are not interaction evidences. Mock publication and experiment for abstract interactions that are not interaction evidences. unspecified method Structural characterization of human heparanase reveals insights into substrate recognition. Structural characterization of human heparanase reveals insights into substrate recognition. Nature structural & molecular biology 2015 imex curation Wu L., Viola CM., Brzozowski AM., Davies GJ. gideon.davies@york.ac.uk 22-Jun-2016: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro cleavage cleavage assay cleavage predetermined predetermined participant predetermined Wu L., Viola CM., Brzozowski AM., Davies GJ. gideon.davies@york.ac.uk Accepted 2016-APR-27 AT 12:23 BST AT 12:23 BST by ORCHARD Nature structural & molecular biology 2015 Only protein-protein interactions imex curation imex curation Structural characterization of human heparanase reveals insights into substrate recognition. Structural characterization of human heparanase reveals insights into substrate recognition. Nature structural & molecular biology 2015 imex curation Wu L., Viola CM., Brzozowski AM., Davies GJ. gideon.davies@york.ac.uk 22-Jun-2016: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Wu L., Viola CM., Brzozowski AM., Davies GJ. gideon.davies@york.ac.uk Accepted 2016-APR-27 AT 12:23 BST AT 12:23 BST by ORCHARD Nature structural & molecular biology 2015 Only protein-protein interactions imex curation imex curation q9y251-pro_0000042260 Heparanase 8 kDa subunit HPSE HEP HPA HPA1 HPR1 HPSE1 HSE1 Endo-glucoronidase Heparanase-1 protein protein human Homo sapiens Human QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKE 36 109 CCD163EC9D4705B2 alpha-d-glcnac-(1->4)-beta-d-glca-(1->4)-alpha-d-glcnac-(1->4)-beta-d-glca-o-pnp alpha-D-GlcNAc-(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNAc-(1->4)-beta-D-GlcA-O-pNP alpha-D-GlcpNAc-(1->4)-c-GlcpA-(1->4)-alpha-D-GlcpNAc-(1->4)-beta-D-GlcpA-O-pNP 4-nitrophenyl alpha-D-N-acetylglucosaminyl-(1->4)-->-glucuronosyl-(1->4)-alpha-D-N-acetylglucosaminyl-(1->4)-->-glucuronic acid GlcNAc-GlcUA-GlcNAc-GlcUA-pNP heparin oligosaccharide dp4, N-acetylated 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucopyranosyl-(1->4)-->-glucopyranuronosyl-(1->4)-2-acetamido-2-deoxy-alpha-D-glucopyranosyl-(1->4)-->-glucopyranosiduronic acid small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) alpha-d-glcns-(1->4)-beta-d-glca-(1->4)-alpha-d-glcns-(1->4)-beta-d-glca-o-pnp alpha-D-GlcNS-(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNS-(1->4)-beta-D-GlcA-O-pNP 4-nitrophenyl 2-deoxy-2-(sulfoamino)-alpha-D-glucosyl-(1->4)-beta-D-glucuronosyl-(1->4)-2-deoxy-2-(sulfoamino)-alpha-D-glucosyl-(1->4)-beta-D-glucuronic acid alpha-D-GlcpNS-(1->4)-beta-D-GlcpA-(1->4)-alpha-D-GlcpNS-(1->4)-beta-D-GlcpA-O-pNP GlcNS-GlcUA-GlcNS-GlcUA-pNP heparin tetrasaccharide, N-sulphated 4-nitrophenyl 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranosyl-(1->4)-beta-D-glucopyranuronosyl-(1->4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranosyl-(1->4)-beta-D-glucopyranosiduronic acid small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) q9y251-pro_0000042262 Heparanase 50 kDa subunit HPSE HEP HPA HPA1 HPR1 HPSE1 HSE1 Endo-glucoronidase Heparanase-1 protein protein human Homo sapiens Human KKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATKEDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI 158 543 3C6EF773788CB1F7 heparin nonasaccharide heparin nonasaccharide,N-sulfated, 6 sulfated beta-D-GlcA-(1->4)-alpha-D-GlcNS-(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNS-(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNS-(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNS(6S)-(1->4)-beta-D-GlcA-O-pNP small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) beta-d-deltahexa(2s)-(1->4)-alpha-d-glcns(6s)-(1->4)-alpha-l-idoa-(1->4)-alpha-d-glcns(6s) beta-D-DeltaHexA(2S)-(1->4)-alpha-D-GlcNS(6S)-(1->4)-alpha-L-IdoA-(1->4)-alpha-D-GlcNS(6S) DeltaHexUA(2S)-GlcNS(6S)-IdoUA(2S)-GlcNS(6S) heparin-derived tetrasaccharide (5xi)-2-O-sulfo-beta-D-xylo-hexopyranuronosyl-(1->4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranosyl-(1->4)-2-O-sulfo-alpha-L-idopyranuronosyl-(1->4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) hpse_human_1-1 3 7 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 4 unspecified role unspecified role neutral component neutral component spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 5 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 2b 1.64 A Rworking 17% Rfree 20% alpha_d_glcns_(1_>4)_beta_d_glca_(1_>4)_alpha_d_glcns_(1_>4)_beta_d_glca_o_pnp-hpse_human_1-1 3 7 unspecified role unspecified role neutral component neutral component region region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 4 unspecified role unspecified role neutral component neutral component spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 6 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 2c 1.63 A Rworking 17%, Rfree 20% beta_d_deltahexa(2s)_(1_>4)_alpha_d_glcns(6s)_(1_>4)_alpha_l_idoa_(1_>4)_alpha_d_glcns(6s)-hpse_human_1-1 3 4 unspecified role unspecified role neutral component neutral component spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 7 unspecified role unspecified role neutral component neutral component region region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 9 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 2e 1.73 A Rworking 17% Rfree 21% hp_dp4-hpse_human_1-1 3 8 unspecified role unspecified role neutral component neutral component pig Sus scrofa (Pig) Pig 4 unspecified role unspecified role neutral component neutral component spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. 7 unspecified role unspecified role neutral component neutral component region region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. direct interaction direct interaction Figure 2d 1.88 A Rworking 18% Rfree 22% hp_dp4-hpse_human_1-2 2 8 enzyme enzyme unspecified role unspecified role 33 enzyme target enzyme target substrate substrate unspecified role unspecified role spofr-sf_21 Spodoptera frugiperda insect cells sf_21 Insect cells derived from immature ovaries of fall armyworm Spodoptera frugiperda pupae. full name: IPLB-SF-21-AE cells are susceptible to Baculovirus infection. cleavage cleavage reaction cleavage Figure 3S hpse_human-1 HPA1 complex Heparanase complex HPSE dimer 4 enzyme enzyme 50 kd binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 7 enzyme enzyme 8 kd binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain 37 35 direct interaction direct interaction human Homo sapiens Human stable complex stable complex physical interaction evidence used in manual assertion physical interaction evidence used in manual assertion IPI inferred from physical interaction An endo-beta-D-glucuronidase of the glycoside hydrolase 79 (GH79) family complex that cleaves the extracellular matrix heparan sulfate proteoglycans (HSPGs) into HS side chains and core proteoglycans. Selectively cleaves the linkage between a glucuronic acid unit and an N-sulfo glucosamine unit of HSPGs carrying either a 3-O-sulfo, a 6-O-sulfo or a 2-O-sulfo group, but not linkages between a glucuronic acid unit and a 2-O-sulfated iduronic acid moiety. HS sulfation serves as a molecular signal that directs heparanase to cleave only certain glycan sites and acts as mechanistic handles by which the enzyme can prize open the substrate HS helix and more effectively access the trisaccharide cleavage site via heparanase-binding induced distortion of the substrate helix. Present in a variety of cellular locations where it performs an essential housekeeping role in catabolic processing of internalized HSPGs and at the cell surface or released into the ECM where it participates in ECM degradation and remodeling. HSPGs ensure that bioactive molecules such as growth factors, chemokines, lipoproteins, and enzymes are localized to the cell surface and ECM and function in the control of normal and pathological processes. These include morphogenesis, osteogenesis, hair follicle inner root sheath differentiation and hair homeostasis, wound healing, shedding of syndecans, inflammation, pre-eclampsia, autoimmunity, cell proliferation and migration associated with metastasis, endothelial invasion and angiogenesis. Cleavage of HSPGs is likely to release these regulators that can alter the functional state of tissues and provide a mechanism by which cells can respond rapidly to changes in the extracellular environment. The proliferative advantages conferred by heparanase lead to its up-regulation in tumors in a variety of tissues, and its over-expression correlates strongly with metastasis and worsened clinical prognoses. Also acts as pro-coagulant by increasing the generation of activation factor X in the presence of tissue factor and activation factor VII. Increases cell adhesion to the extracellular matrix (ECM) independent of its enzymatic activity. HPSE is the only mammalian gene so far identified to have heparanase activity. Secreted as a latent enzyme and internalized into late endosomes or lysosomes where it is subjected to proteolytic cleavage and activation. Cleavage at Glu109-Ser110 and Gln157-Lys158 yields an N-terminal 8 kDa and a C-terminal 50 kDa polypeptide that combine to form the catalytic site. Subsequent exocytosis transports the heparanase to its target sites. Prior to cleavage, the linker between the the 8 kD and 50 kD proteolytic chains acts as a steric block. Residues Glu-225 and Glu-343, located in the catalytic cleft, are crucial for its heparanase activity having been identified as the catalytic nucleophile and acid-base of HPSE. Heterodimer heparin (CHEBI:28304) calcium atom (CHEBI:22984) magnesium atom (CHEBI:25107) Cancer [EFO:0000311]: upregulation of heparanase enhances tumor progression, metastatic development and cellular invasion in a variety of cancers. Pre-eclampsia [EFO:0000668]: A complication of pregnancy, characterized by a complex of symptoms including maternal hypertension and proteinuria with or without pathological edema. Symptoms may range between mild and severe. Pre-eclampsia usually occurs after the 20th week of gestation, but may develop before this time in the presence of trophoblastic disease. Sylvie Ricard-Blum, MatrixDB, Lyon Accepted 2016-MAR-07 by ORCHARD