Proteinase

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function Proteinase (PRO) are enzymes which hydrolyze peptide bonds. They are classified by the amino acid site of their cleavage or by the pH at which they are active. PRO B is a serine protease. For more details see Streptomyces griseus proteinase B. PRO A is a carboxylproteinase. PRO K is a serine protease which cleaves proteins preferentially after hydrophobic residues. Calcium ions contribute to the stability of the enzyme. PRO K is active over a wide pH range and is used in molecular biology to inactivate nucleases from preparations of DNA or RNA. PRO K is used in the partial proteolysis of lactoferrin into its N- and C-lobe. The two lobes of lactoferrin have different antimicrobial and antifungal properties. PRO K can digest hair (keratin). For cysteine PRO from Trypanosoma cruzi see Cruzain. The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen-bond density in the reactive loop Background: Plant proteinase Inhibitors (PIs) are ubiquitous in the plant kingdom and have been extensively studied as plant defense molecules, which inhibit hydrolytic enzymes (e.g. trypsin, colored in darkmagenta) of the insect gut . Among various PI families, Serine PI Pin-II/Pot-II family displays a remarkable structural and functional diversity at the gene and protein level . Wound, herbivory and stress induced up-regulation of these PIs clearly link them to plant defense . Previous studies using transgenic systems or in vivo assays have positively correlated the advantage offered by Pin-II PI expression in plants against insect attack . Precursor proteins of Pin-II PIs consist of 1- to 8- inhibitory repeat domains (IRDs) connected by proteolytic-sensitive linkers, which releases IRD units upon cleavage. Each IRD is a peptide of around 50 aa length (colored in green) with a molecular mass of ~6 KDa. The aa sequence of IRDs shows variations, at the same time the 8 cysteine residues that form disulfide bridge are conserved (colored in yellow) . One structural feature of Pin-II IRD is a disordered loop with triple stranded β sheet scaffold. The disordered solvent exposed reactive loop is anchored by the four conserved disulfide bonds (C4-C41, C7-C25, C8-C37 and C14-C50) . Among the four disulfide bonds, C8-C37 has been found to be very crucial for maintaining active conformation, whereas C4-C41 has an important role in maintaining the flexibility of the reactive loop . Thus, any selective loss of disulfide bond is expected to have evolutionary significance leading to functional differentiation of inhibitors . [A] Functionality: To assess the effect of aa variations on activity and structural stability different biochemical studies and 20 ns MD simulations was performed on IRD structures. Inhibition kinetic studies displayed a sigmoidal pattern with increasing concentrations of the inhibitors suggesting reversible and competitive inhibition with tight binding. IRD-9 turned out to be a stronger inhibitor of bovine trypsin (IC50 ~0.0022 mM) than IRD-7 (IC50 ~0.135 mM) and IRD-12 (IC50 ~0.065 mM). [B] Structural Variability: In accordance with the structure of a typical IRD belonging to Pin-II PI family, the predicted structures of CanPI also have three antiparallel β sheets joined by disordered loops containing the reactive site and stabilized by four disulfide bonds. It was thought that the disulfide bonds act as structural scaffold to hold the reactive site in a relatively rigid conformation and provide thermal and proteolytic stability. A single 310-helix of one turn is also present in the structure, the disordered loop is held by disulfide bond in IRD-7 and -12 whereas by a network of intra molecular hydrogen bonds in IRD-9. IRD-7 (colored in salmon) and IRD-12 (in deeppink) have 4 disulfide bonds, whereas IRD-9 (in magenta) has only 2 disulfide bonds. Furthermore, post-simulation analysis of the intramolecular hydrogen bonds illustrated that IRD-9 with two disulfide bonds (C7-C25 and C8-C37) less, has a relatively higher density of intra-molecular hydrogen bonds as compared to IRD-7 and -12. These intramolecular hydrogen bonds might be substituting the two lost disulfide bonds of IRD-9 to stabilize the protein structure in the active conformation and might be protecting the molecules from a hydrophobic collapse. The replaced serine residues in the place of two cysteines C7 and C8 in IRD-9 may be contributing to the increased number of hydrogen bonds. [C] The molecular models of the IRD bound HaTry predicted several atomic interactions with a reactive loop of inhibitors that also explained the contribution of the solvent exposed reactive loop. There are several hydrogen bonds in the IRD-9-HaTry complex. ARG-39 from IRD-12 reactive site formed two hydrogen bonds with the residues of the HaTry active site. In case of IRD-7, side chain of LYS-39 residue of reactive loop form one hydrogen bond each, with carboxyl oxygen atom of HIS-50. MD simulations provides structural insight into an importance of inter/intra molecular hydrogen bonds and its effect on the interaction between protease and PIs. The results of this analysis were corroborated with previous reports. Post simulation analysis also explained experimentally observed increase in binding affinity, hence activity of IRD-9 towards proteases. See also . 3D structures of proteinase Proteinase 3D structures

3D structures of proteinase

Updated on 11-October-2020

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• Proteinase A or saccharopepsin
  • Streptomyces griseus proteinase B, Cruzain, Proteinase 3D structures – yPRO - yeast
    
  • 1dp5, 1dpj, 1g0v - yPRO + polypeptide inhibitor IA3
    
  • 1fq5, 1fq6, 1fq7, 1fq8 - yPRO + inhibitor
    
  • 2sga – SgPRO – Streptomyces griseus
    
  • 1sgc - SgPRO + chymostatin A
    
  • 3sga, 4sga, 5sga - SgPRO + polypeptide inhibitor
    
  • 4fvd – hevPRO 2A + peptide – human enterovirus
    
  • 4fvb – hevPRO 2A (mutant)
    
• Proteinase B
  • 3sgb – SgPRO + turkey ovomucoid inhibitor
    
  • 1sgp, 1sgq, 1sgr, 1cso, 1ct0, 1ct2, 1ct4, 1ds2, 2sgp, 2nu3, 2nu4 – SgPRO + turkey ovomucoid inhibitor (mutant)
    
  • 4sgb - SgPRO + potato inhibitor
• Proteinase K
  • 2prk, 1cnm, 1egq, 2id8, 2g4v, 2v8b, 3gt3, 3gt4, 3d9q, 3ddz, 3de0, 3de1, 3de2, 3de3, 3de4, 3de5, 3de6, 3de7, 3dvq, 3dvr, 3dvs, 3dw1, 3dw3, 3dwe, 3i2y, 3i30, 3i37, 3i34, 3l1k, 3aj8, 3aj9, 3q40, 3q5g, 3qmp, 4b5l, 4fon, 6rzp, 6qf1, 6pu5, 6pu4, 6pkt, 6pks, 6pkr, 6pkq, 6pkp, 6pko, 6pkn, 6pkm, 6pkl, 6pkk, 6pkj, 6n4u, 6mh6, 6fjs, 6clb, 6cla, 6cl9, 6cl8, 6cl7, 5wjh, 5wjg, 5whw, 5uvl, 6txg, 6pq0, 6pq4, 6k2v, 6k2x, 6k2w, 6k2p, 6k2r, 6k2t, 6k2s, 6v8r, 6law – EaPRO + Ca – Engyodontium album
    
  • 1ic6, 6qxv – EaPRO (mutant) + Ca
    
  • 1ptk, 1ht3 – EaPRO + Ca + Hg
    
  • 2pkc – EaPRO + Na
    
  • 5wrc – EaPRO + Pr
    
  • 4dj5, 4woc, 4wob – EaPRO
    
• Proteinase K complex with peptide
  • 3prk, 1p7v, 1p7w – EaPRO + Ca + peptide inhibitor
    
  • 1bjr, 2dqk, 2duj – EaPRO + Ca + lactoferrin peptide
    
  • 2hd4 – EaPRO + Ca + lactoferrin peptide inhibitor
    
  • 2dp4, 3ptl – EaPRO + lactoferrin peptide
    
  • 1pek, 1pfg, 4zar – EaPRO + peptide inhibitor
    
  • 1pj8 – EaPRO + Hg + substrate analog peptide
    
  • 2hpz, 2pq2, 6kkf – EaPRO + Ca + peptide
    
  • 3osz – EaPRO + Ca + antimicrobial peptide
    
  • 2b6n – PRO + tripeptide - Serratia
    
• Proteinase K complex with small molecule
  • 2pwb – EaPRO + Ca + coumarin
    
  • 2pyz – EaPRO + Ca + auramine
    
  • 2pwa – EaPRO + Ca + alanine boronic acid
    
  • 1oyo – EaPRO + Ca + melanin monomer
    
  • 3dyb – EaPRO + Ca + digalacturonic acid
    
  • 6rvg, 6rve, 6ruw, 6run, 6ruk, 6ruh, 6rug – EaPRO + keggin derivative
    
• Proteinase 3C
  • 1qa7 – PRO – Hepatitis virus
    
  • 2vb0, 3zyd - PRO – Coxsakievirus
    
  • 3zye – csvPRO (mutant)
    
  • 3zzd, 3zzc, 3zza, 3zzb, 3zz8, 3zz9, 3zz7, 3zz5, 3zz3, 3zz4 – csvPRO (mutant) + inhibitor
    
  • 4ghq – hevPRO
    
  • 4ght – hevPRO + common cold drug
    
  • 5c1u, 5c1x, 5c1y, 5c20, 5dp9, 5dp3, 5dp5, 5dp8, 5dp7, 5dpa, 5dp4, 5dp6 – PRO + inhibitor – Enterovirus
    
• H2-Proteinase
  • 1wni – PRO – Trimeresurus flavoviridis
• Aspartic Proteinase
  • 1fq4 - yPRO + inhibitor
    
  • 2asi – PRO – Rhizomucor miehei
    
  • 2apr – RmPRO – Rhizopus microsporus
    
  • 3apr - RmPRO + reduced peptide inhibitor
    
  • 5apr, 4apr - RmPRO + renin inhibitor
    
  • 6apr - RmPRO + pepstatin
    
  • 1zap, 2h6s – CaPRO – Candida albicans
    
  • 1eag – CaPRO + inhibitor
    
  • 1izd - AoPRO – Aspergillus oryzae
    
  • 1ize - AoPRO + polypeptide-statin inhibitor
    
  • 1j71 - PRO + polypeptide inhibitor – Candida tropicalis
    
  • 1wkr - PRO + polypeptide-statin inhibitor – Irpex lacteus
    
  • 3c9x - TrPRO – Trichoderma reesi
    
  • 3emy - TrPRO + pepstatin
    
• Aspartic Proteinase Endothiapepsin
  • 3urj, 1oew, 4ape - CpPRO – Cryphonectria parasitica
    
  • 4er4, 1eed, 2er7, 5er1 - CpPRO + renin inhibitor
    
  • 1epo, 1gvv, 2jji, 2jjj, 1epr, 1epq, 1epp, 1epn, 1epm, 1epl, 1gvw, 1gvt, 1gvx, 1gvu, 1oex, 3er3, 4er1, 6scv, 6ron, 6rsv, 1ent - CpPRO + inhibitor
    
  • 3uri, 3url, 1er8, 2er6, 4lp9, 5er2, 3er5 - CpPRO + peptide inhibitor
    
  • 2vs2, 1gkt - CpPRO + inhibitor - Neutron diffraction
    
  • 2er0, 2er9 - CpPRO + statin-inhibitor
    
  • 4er2 - CpPRO + pepstatin
    
• Cysteine Proteinase or gingipain
  • 2e03, 2e02, 2e01, 2e00, 2dzz, 2dzy – yPRO 1 (mutant)
    
  • 2hrv – PRO 2A – human rhinovirus
    
  • 3m1h, 4itc – PgPRO adhesion domain residues 982-1154 – Porphyromonas gingivalis
    
  • 4rbm, 4tkx – PgPRO catalytic domain residues 229-683
    
  • 6i9a – PgPRO catalytic domain + inhibitor
    
  • 5mun – PgPRO residues 20-228
    
  • 2fo5 – PRO residues 133-356 + leupeptin – Hordenum vulgare
    
  • 1x9y – SaPRO – Staphylococcus aureus
    
  • 1y4h, 1pxv – SaPRO + PRO inhibitor
    
  • 6p4e – PRO + inhibitor – Leishmnia mexicana
    
• Cysteine Proteinase or falcipain
  • 2ghu – PfPRO-2 – Plasmodium falciparum
    
  • 3bpf, 6ssz, 6jw9 – PfPRO-2 + inhibitor
    
  • 3pnr – PfPRO-2 + PblCP-C
    
  • 1yvb – PfPRO-2 + cystatin
    
  • 2oul – PfPRO-2 + chagasin
    
  • 3bpm – PfPRO-3 + leupeptin
    
  • 3bwk – PfPRO-3 + inhibitor
    
• Serine Proteinase
  • 5m3n, 1lcy – hPRO HTRA2 – human
    
  • 5fht, 5m3o, 5tny, 5tnz, 5to0, 5to1, 5wyn – hPRO HTRA2 (mutant)
    
  • 3s9a, 3s9b – RvPRO – Siamese Russell’s viper
    
  • 3s9c, 3sbk – RvPRO + human factor V polypeptide
    
  • 1po0, 1op2 – PRO – Chinese moccasin
    
  • 1qy8 – SaPRO
    
  • 1mbm – PRO – equine arteritis virus
    
  • 1dbi – PRO – Bacillus
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  • 1ga1, 1ga4, 1ga6, 1nlu – PsPRO + iodotyrostatin fragment – Pseudomonas
    
  • 6m8w, 6m8y, 6m8f, 6m9c, 6m9d - PsPRO + polypeptide inhibitor
    
  • 1s2n, 1sh7 – PRO – Vibrio
    
• Astacin
  • 1iac, 1iad, 1iae, 1iab, 1iaa, 1ast – cAst – crayfish
    
  • 3lq0 – cpro-Ast
    
  • 6saz, 6ht9 – cAst + fetuin-B
    
  • 1qji, 1qjj – cAst + inhibitor
    

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Alexander Berchansky, Michal Harel, Joel L. Sussman, Karsten Theis