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<StructureSection load='' size='350' side='right' scene='Journal:JBSD:39/Cv/11' caption=''>
<StructureSection load='' size='350' side='right' scene='Journal:JBSD:39/Cv/11' caption=''>
__TOC__
==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.<br />
'''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.<br />
*  '''PRO B''' is a serine protease<ref>PMID:3325823</ref>.  For more details see [[Streptomyces griseus proteinase B]].<br />
*  '''PRO B''' is a serine protease<ref>PMID:3325823</ref>.  For more details see [[Streptomyces griseus proteinase B]].<br />
*  '''PRO A''' is a carboxylproteinase<ref>PMID:6799292</ref>.<br />
*  '''PRO A''' is a carboxylproteinase<ref>PMID:6799292</ref>.<br />
*  '''PRO K''' is a serine protease which cleaves proteins preferentially after hydrophobic residues<ref>PMID:9606141</ref>.  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).
*  '''PRO K''' is a serine protease which cleaves proteins preferentially after hydrophobic residues<ref>PMID:9606141</ref>.  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).<br />
For cysteine PRO from ''Trypanosoma cruzi'' see [[Cruzain]].
*'''Endothiapepsin''' is an '''aspartic PRO''' from ''Cryphonectria parasitica''<ref>PMID:1525155</ref>.<br />
*'''Saccharopepsin''' is an '''aspartic PRO''' from yeast<ref>PMID:17447722</ref>.<br />
*'''Falcipain''' is an '''cystein PRO''' from ''Plasmodium falciparum''<ref>PMID:21660657</ref>.<br />
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 <ref>doi 10.1080/07391102.2012.745378</ref> ===
==3D structures of proteinase==
 
[[Proteinase 3D structures]]
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.'' <scene name='Journal:JBSD:39/Cv/12'>trypsin</scene>, <font color='darkmagenta'><b>colored in darkmagenta</b></font>) of the insect gut <ref name="Green">PMID: 17836138</ref>. Among various PI families, Serine PI Pin-II/Pot-II family displays a remarkable structural and functional diversity at the gene and protein level <ref name="Kong">PMID: 18315854</ref>. Wound, herbivory and stress induced up-regulation of these PIs clearly link them to plant defense <ref name="Green">PMID: 17836138</ref>. 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 <ref name="Johnson">PMID: 2602379</ref> <ref name="Duan">PMID: 9630927</ref>. Precursor proteins of Pin-II PIs consist of 1- to 8- <scene name='Journal:JBSD:39/Cv/4'>inhibitory repeat domains (IRDs)</scene> connected by proteolytic-sensitive linkers, which releases IRD units upon cleavage.  <scene name='Journal:JBSD:39/Cv/5'>Each IRD is a peptide of around 50 aa length</scene> (<span style="color:lime;background-color:black;font-weight:bold;">colored in green</span>) with a molecular mass of ~6 KDa. The aa sequence of IRDs shows variations, at the same time the <scene name='Journal:JBSD:39/Cv/6'>8 cysteine residues that form disulfide bridge are conserved</scene> (<span style="color:yellow;background-color:black;font-weight:bold;">colored in yellow</span>) <ref name="Nielsen">PMID: 7578034</ref> <ref name="Scanlon">PMID: 10425681</ref> <ref name="Lee">PMID: 10360353</ref> <ref name="Schirra">PMID: 11178894</ref>. One structural feature of Pin-II IRD is a disordered loop with triple stranded &#946; 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) <ref name="Schirra1">PMID: 16029154</ref> <ref name="Schirra2">PMID: 18991765</ref>. 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 <ref name="Schirra3">PMID: 19925809</ref>. Thus, any selective loss of disulfide bond is expected to have evolutionary significance leading to functional differentiation of inhibitors <ref name="Li">PMID: 21494600</ref>.


[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] <scene name='Journal:JBSD:39/Cv/16'>Structural Variability</scene>: In accordance with the structure of a typical IRD belonging to Pin-II PI family, the predicted structures of CanPI also  have  <scene name='Journal:JBSD:39/Cv/7'>three  antiparallel  &#946;  sheets  joined  by  disordered  loops  containing  the reactive site and stabilized by four disulfide bonds</scene>. 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 3<sub>10</sub>-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. <scene name='Journal:JBSD:39/Cv/13'>IRD-7</scene> <span style="color:salmon;background-color:black;font-weight:bold;">(colored in salmon)</span> and <scene name='Journal:JBSD:39/Cv/9'>IRD-12</scene> <span style="color:deeppink;background-color:black;font-weight:bold;">(in deeppink)</span> have 4 disulfide bonds, whereas <scene name='Journal:JBSD:39/Cv/14'>IRD-9</scene> <font color='magenta'><b>(in magenta)</b></font> 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 <scene name='Journal:JBSD:39/Ird9/3'>IRD-9-HaTry complex</scene>. ARG-39 from <scene name='Journal:JBSD:39/Cv/17'>IRD-12</scene> reactive site formed two hydrogen bonds with the residues of the HaTry active site. In <scene name='Journal:JBSD:39/Ird9/2'>case of IRD-7</scene>, 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 <ref name="Barrette-Ng">PMID: 12684499</ref> <ref name="Dunse">PMID: 20696921</ref> <ref name="Tamhane">PMID: 19393726</ref> <ref name="Tamhane1">PMID: 15715970</ref>.
</StructureSection>
</StructureSection>
==3D structures of proteinase==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
*'''Proteinase A or saccharopepsin'''
**[[2sga]] – SgPRO – ''Streptomyces griseus''<br />
**[[2jxr]], [[1fmu]], [[1fmx]] – yPRO - yeast<br />
**[[1sgc]] - SgPRO + chymostatin A<br />
**[[3sga]], [[4sga]], [[5sga]] - SgPRO + polypeptide inhibitor<br />
**[[1dp5]], [[1dpj]], [[1g0v]] - yPRO + polypeptide inhibitor IA3<br />
**[[1fq5]], [[1fq6]], [[1fq7]], [[1fq8]] - yPRO + inhibitor<br />
**[[4fvd]] – hevPRO 2A + peptide – human enterovirus <br />
**[[4fvb]] – hevPRO 2A (mutant) <br />
*'''Proteinase B'''
**[[3sgb]] – SgPRO + turkey ovomucoid inhibitor<br />
**[[1sgp]], [[1sgq]], [[1sgr]], [[1cso]], [[1ct0]], [[1ct2]], [[1ct4]], [[1ds2]], [[2sgp]], [[2nu3]], [[2nu4]] – SgPRO + turkey ovomucoid inhibitor (mutant)<br />
**[[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]] – EaPRO + Ca – ''Engyodontium album'' <br />
**[[1ic6]] – EaPRO (mutant) + Ca  <br />
**[[1ptk]], [[1ht3]] – EaPRO + Ca + Hg <br />
**[[2pkc]] – EaPRO + Na  <br />
**[[4dj5]], [[4woc]], [[4wob]] – EaPRO  <br />
*Proteinase K complex with peptide
**[[3prk]], [[1p7v]], [[1p7w]] – EaPRO + Ca + peptide inhibitor  <br />
**[[1bjr]], [[2dqk]], [[2duj]] – EaPRO + Ca + lactoferrin peptide  <br />
**[[2hd4]] – EaPRO + Ca + lactoferrin peptide inhibitor<br />
**[[2dp4]], [[3ptl]] – EaPRO + lactoferrin peptide  <br />
**[[1pek]], [[1pfg]], [[4zar]] – EaPRO + peptide inhibitor  <br />
**[[1pj8]] – EaPRO + Hg + substrate analog peptide  <br />
**[[2hpz]], [[2pq2]] – EaPRO + Ca + peptide  <br />
**[[3osz]] – EaPRO + Ca + antimicrobial peptide  <br />
**[[2b6n]] – PRO + tripeptide - ''Serratia''<br />
*Proteinase K complex with small molecule
**[[2pwb]] – EaPRO + Ca + coumarin  <br />
**[[2pyz]] – EaPRO + Ca + auramine  <br />
**[[2pwa]] – EaPRO + Ca + alanine boronic acid  <br />
**[[1oyo]] – EaPRO + Ca + melanin monomer  <br />
**[[3dyb]] – EaPRO + Ca + digalacturonic acid  <br />
*'''Proteinase 3C'''
**[[1qa7]] – PRO – Hepatitis virus<br />
**[[2vb0]], [[3zyd]] - PRO – Coxsakievirus<br />
**[[3zye]] – csvPRO (mutant) <br />
**[[3zzd]], [[3zzc]], [[3zza]], [[3zzb]], [[3zz8]], [[3zz9]], [[3zz7]], [[3zz5]], [[3zz3]], [[3zz4]] – csvPRO (mutant) + inhibitor <br />
**[[4ghq]] – hevPRO  <br />
**[[4ght]] – hevPRO + common cold drug  <br />
*'''H2-Proteinase'''
**[[1wni]] – PRO – ''Trimeresurus flavoviridis''
*'''Aspartic Proteinase'''
**[[2asi]] – PRO – ''Rhizomucor miehei''<br />
**[[1zap]] – CaPRO – ''Candida albicans''<br />
**[[1izd]] - AoPRO – ''Aspergillus oryzae''<br />
**[[1eag]] – CaPRO + inhibitor <br />
**[[1fq4]] - yPRO + inhibitor<br />
**[[1j71]] - PRO + polypeptide inhibitor – ''Candida tropicalis''<br />
**[[1ize]] - AoPRO + polypeptide-statin inhibitor<br />
**[[1wkr]] - PRO + polypeptide-statin inhibitor – ''Irpex lacteus''
*'''Cysteine Proteinase''' or '''gingipain'''
**[[2hrv]] – PRO 2A – human rhinovirus<br />
**[[3m1h]], [[4itc]] – PgPRO adhesion domain residues 982-1154 – ''Porphyromonas gingivalis'' <br />
**[[4rbm]], [[4tkx]] – PgPRO catalytic domain residues 229-683<br />
**[[5mun]] – PgPRO residues 20-228 <br />
**[[2fo5]] – PRO residues 133-356 + leupeptin – ''Hordenum vulgare'' <br />
**[[2e03]], [[2e02]], [[2e01]], [[2e00]], [[2dzz]], [[2dzy]] – yPRO 1 (mutant) <br />
**[[1x9y]] – SaPRO – ''Staphylococcus aureus'' <br />
**[[1y4h]], [[1pxv]] – SaPRO + PRO inhibitor <br />
*'''Serine Proteinase'''
**[[1s2n]], [[1sh7]] – PRO – ''Vibrio''<br />
**[[3s9a]], [[3s9b]] – RvPRO – Siamese Russell’s viper<br />
**[[1po0]], [[1op2]] – PRO – Chinese moccasin <br />
**[[1qy8]] – SaPRO <br />
**[[1mbm]] – PRO – equine arteritis virus <br />
**[[1dbi]] – PRO – ''Bacillus'' <br />
**[[3s9c]], [[3sbk]] – RvPRO + human factor V polypeptide<br />
**[[1ga1]], [[1ga4]], [[1ga6]], [[1nlu]] – PsPRO + iodotyrostatin fragment – ''Pseudomonas''<br />
**[[1kdv]], [[1kdy]], [[1kdz]], [[1ke1]], [[1ke2]] - PsPRO + polypeptide inhibitor<br />
**[[5m3n]], [[1lcy]] – hPRO HTRA2 – human <br />
**[[5fht]], [[5m3o]], [[5tny]], [[5tnz]], [[5to0]], [[5to1]], [[5wyn]] – hPRO HTRA2 (mutant) <br />
}}


== References ==
== References ==
<references/>
<references/>
[[Category: Topic Page]]
[[Category: Topic Page]]

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