7am4 - Revision history

OCA at 07:45, 1 May 2024

2024-05-01T07:45:00Z

←Older revision		Revision as of 07:45, 1 May 2024
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	<StructureSection load='7am4' size='340' side='right'caption='[[7am4]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='7am4' size='340' side='right'caption='[[7am4]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7am4]] 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=7AM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7am4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM4 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.81Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[7am3\|7am3]]~~</~~div~~><~~/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=7am4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am4 OCA], [https://pdbe.org/7am4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am4 RCSB], [https://www.ebi.ac.uk/pdbsum/7am4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am4 ProSAT]</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=7am4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am4 OCA], [https://pdbe.org/7am4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am4 RCSB], [https://www.ebi.ac.uk/pdbsum/7am4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>	+	[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>	+	==See Also==
-		+	*[[Subtilisin 3D structures\|Subtilisin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 7am4" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus amyloliquefaciens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Subtilisin]]~~	+	[[Category: Janssen DJ]]
-	[[Category: Janssen~~, D J~~]]	+	[[Category: Rozeboom HJ]]
-	[[Category: Rozeboom~~, H J]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Peptide ligase~~]]	+

OCA at 06:51, 24 March 2021

2021-03-24T06:51:34Z

←Older revision		Revision as of 06:51, 24 March 2021
Line 1:		Line 1:

	==Crystal structure of Peptiligase mutant - L217H/M222P==		==Crystal structure of Peptiligase mutant - L217H/M222P==
-	<StructureSection load='7am4' size='340' side='right'caption='[[7am4]]' scene=''>	+	<StructureSection load='7am4' size='340' side='right'caption='[[7am4]], [[Resolution\|resolution]] 1.81Å' 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=7AM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7am4]] 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=7AM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM4 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=7am4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am4 OCA], [https://pdbe.org/7am4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am4 RCSB], [https://www.ebi.ac.uk/pdbsum/7am4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am4 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7am3\|7am3]]</div></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=7am4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am4 OCA], [https://pdbe.org/7am4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am4 RCSB], [https://www.ebi.ac.uk/pdbsum/7am4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am4 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 7am4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Janssen DJ]]	+	[[Category: Subtilisin]]
-	[[Category: Rozeboom HJ]]	+	[[Category: Janssen, D J]]
		+	[[Category: Rozeboom, H J]]
		+	[[Category: Ligase]]
		+	[[Category: Peptide ligase]]

OCA at 10:00, 17 February 2021

2021-02-17T10:00:45Z

←Older revision		Revision as of 10:00, 17 February 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7am4 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Peptiligase mutant - L217H/M222P==
-		+	<StructureSection load='7am4' size='340' side='right'caption='[[7am4]]' scene=''>
-	~~Authors~~: ~~Rozeboom~~, H.J., ~~Janssen~~, D.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AM4 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Peptiligase mutant~~ -~~L217H~~/~~M222P~~	+	</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=7am4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7am4 OCA], [https://pdbe.org/7am4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7am4 RCSB], [https://www.ebi.ac.uk/pdbsum/7am4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7am4 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Janssen~~, D.J~~]]	+	__TOC__
-	[[Category: Rozeboom~~, H.J~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Janssen DJ]]
		+	[[Category: Rozeboom HJ]]

OCA at 05:18, 4 November 2020

2020-11-04T05:18:15Z

←Older revision		Revision as of 05:18, 4 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7am4 is ON HOLD	+	The entry 7am4 is ON HOLD until Paper Publication

	Authors: Rozeboom, H.J., Janssen, D.J.		Authors: Rozeboom, H.J., Janssen, D.J.

OCA at 18:54, 28 October 2020

2020-10-28T18:54:57Z

←Older revision		Revision as of 18:54, 28 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7am4 is ON HOLD ~~until sometime in the future~~	+	The entry 7am4 is ON HOLD

	Authors: Rozeboom, H.J., Janssen, D.J.		Authors: Rozeboom, H.J., Janssen, D.J.

OCA at 06:35, 21 October 2020

2020-10-21T06:35:16Z

←Older revision		Revision as of 06:35, 21 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7am4 is ON HOLD	+	The entry 7am4 is ON HOLD until sometime in the future

	Authors: Rozeboom, H.J., Janssen, D.J.		Authors: Rozeboom, H.J., Janssen, D.J.

OCA: Protected "7am4" [edit=sysop:move=sysop]

2020-10-14T04:05:48Z

Protected "7am4" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:05, 14 October 2020

OCA: New page: '''Unreleased structure''' The entry 7am4 is ON HOLD Authors: Rozeboom, H.J., Janssen, D.J. Description: Crystal structure of Peptiligase mutant -L217H/M222P [[Category: Unreleased Str...

2020-10-14T04:05:47Z

New page: '''Unreleased structure''' The entry 7am4 is ON HOLD Authors: Rozeboom, H.J., Janssen, D.J. Description: Crystal structure of Peptiligase mutant -L217H/M222P [[Category: Unreleased Str...

New page

'''Unreleased structure'''

The entry 7am4 is ON HOLD

Authors: Rozeboom, H.J., Janssen, D.J.

Description: Crystal structure of Peptiligase mutant -L217H/M222P
[[Category: Unreleased Structures]]
[[Category: Janssen, D.J]]
[[Category: Rozeboom, H.J]]