7am3: Difference between revisions
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==Crystal structure of Peptiligase mutant - M222P== | ==Crystal structure of Peptiligase mutant - M222P== | ||
<StructureSection load='7am3' size='340' side='right'caption='[[7am3]]' scene=''> | <StructureSection load='7am3' size='340' side='right'caption='[[7am3]], [[Resolution|resolution]] 1.61Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM3 FirstGlance]. <br> | <table><tr><td colspan='2'>[[7am3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_amyloliquifaciens"_(sic)_fukumoto_1943 "bacillus amyloliquifaciens" (sic) fukumoto 1943]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM3 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7am3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am3 OCA], [https://pdbe.org/7am3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am3 RCSB], [https://www.ebi.ac.uk/pdbsum/7am3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am3 ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apr ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1390 "Bacillus amyloliquifaciens" (sic) Fukumoto 1943])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7am3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am3 OCA], [https://pdbe.org/7am3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am3 RCSB], [https://www.ebi.ac.uk/pdbsum/7am3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am3 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[https://www.uniprot.org/uniprot/SUBT_BACAM SUBT_BACAM]] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.<ref>PMID:12524032</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Omniligase-1 is a broadly applicable enzyme for peptide bond formation between an activated acyl donor peptide and a non-protected acyl acceptor peptide. The enzyme is derived from an earlier subtilisin variant called peptiligase by several rounds of protein engineering aimed at increasing synthetic yields and substrate range. To examine the contribution of individual mutations on S/H ratio and substrate scope in peptide synthesis, we selected peptiligase variant M222P/L217H as a starting enzyme and introduced successive mutations. Mutation A225N in the S1' pocket and F189W of the S2' pocket increased the synthesis to hydrolysis (S/H) ratio and overall coupling efficiency, whereas the I107V mutation was added to S4 pocket to increase the reaction rate. The final omniligase variants appeared to have a very broad substrate range, coupling more than 250 peptides in a 400-member library of acyl acceptors, as indicated by a high-throughput FRET assay. Crystal structures and computational modelling could rationalize the exceptional properties of omniligase-1 in peptide synthesis. | |||
From thiol-subtilisin to omniligase: Design and structure of a broadly applicable peptide ligase.,Toplak A, Teixeira de Oliveira EF, Schmidt M, Rozeboom HJ, Wijma HJ, Meekels LKM, de Visser R, Janssen DB, Nuijens T Comput Struct Biotechnol J. 2021 Feb 9;19:1277-1287. doi:, 10.1016/j.csbj.2021.02.002. eCollection 2021. PMID:33717424<ref>PMID:33717424</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7am3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Janssen | [[Category: Subtilisin]] | ||
[[Category: Rozeboom | [[Category: Janssen, D J]] | ||
[[Category: Rozeboom, H J]] | |||
[[Category: Ligase]] | |||
[[Category: Peptide ligase]] | |||
Revision as of 09:51, 24 March 2021
Crystal structure of Peptiligase mutant - M222PCrystal structure of Peptiligase mutant - M222P
Structural highlights
Function[SUBT_BACAM] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.[1] Publication Abstract from PubMedOmniligase-1 is a broadly applicable enzyme for peptide bond formation between an activated acyl donor peptide and a non-protected acyl acceptor peptide. The enzyme is derived from an earlier subtilisin variant called peptiligase by several rounds of protein engineering aimed at increasing synthetic yields and substrate range. To examine the contribution of individual mutations on S/H ratio and substrate scope in peptide synthesis, we selected peptiligase variant M222P/L217H as a starting enzyme and introduced successive mutations. Mutation A225N in the S1' pocket and F189W of the S2' pocket increased the synthesis to hydrolysis (S/H) ratio and overall coupling efficiency, whereas the I107V mutation was added to S4 pocket to increase the reaction rate. The final omniligase variants appeared to have a very broad substrate range, coupling more than 250 peptides in a 400-member library of acyl acceptors, as indicated by a high-throughput FRET assay. Crystal structures and computational modelling could rationalize the exceptional properties of omniligase-1 in peptide synthesis. From thiol-subtilisin to omniligase: Design and structure of a broadly applicable peptide ligase.,Toplak A, Teixeira de Oliveira EF, Schmidt M, Rozeboom HJ, Wijma HJ, Meekels LKM, de Visser R, Janssen DB, Nuijens T Comput Struct Biotechnol J. 2021 Feb 9;19:1277-1287. doi:, 10.1016/j.csbj.2021.02.002. eCollection 2021. PMID:33717424[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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