8b2f - Revision history

OCA at 08:15, 7 February 2024

OCA — Wed, 07 Feb 2024 08:15:42 GMT

←Older revision		Revision as of 08:15, 7 February 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8b2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2f OCA], [https://pdbe.org/8b2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2f RCSB], [https://www.ebi.ac.uk/pdbsum/8b2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2f 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=8b2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2f OCA], [https://pdbe.org/8b2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2f RCSB], [https://www.ebi.ac.uk/pdbsum/8b2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2f ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Muramidases (also known as lysozymes) hydrolyse the peptidoglycan component of the bacterial cell wall and are found in many glycoside hydrolase (GH) families. Similar to other glycoside hydrolases, muramidases sometimes have noncatalytic domains that facilitate their interaction with the substrate. Here, the identification, characterization and X-ray structure of a novel fungal GH24 muramidase from Trichophaea saccata is first described, in which an SH3-like cell-wall-binding domain (CWBD) was identified by structure comparison in addition to its catalytic domain. Further, a complex between a triglycine peptide and the CWBD from T. saccata is presented that shows a possible anchor point of the peptidoglycan on the CWBD. A ;domain-walking' approach, searching for other sequences with a domain of unknown function appended to the CWBD, was then used to identify a group of fungal muramidases that also contain homologous SH3-like cell-wall-binding modules, the catalytic domains of which define a new GH family. The properties of some representative members of this family are described as well as X-ray structures of the independent catalytic and SH3-like domains of the Kionochaeta sp., Thermothielavioides terrestris and Penicillium virgatum enzymes. This work confirms the power of the module-walking approach, extends the library of known GH families and adds a new noncatalytic module to the muramidase arsenal.
-
-	Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases.,Moroz OV, Blagova E, Lebedev AA, Skov LK, Pache RA, Schnorr KM, Kiemer L, Friis EP, Nymand-Grarup S, Ming L, Ye L, Klausen M, Cohn MT, Schmidt EGW, Davies GJ, Wilson KS Acta Crystallogr D Struct Biol. 2023 Aug 1. doi: 10.1107/S2059798323005004. PMID:37428847<ref>PMID:37428847</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8b2f" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:10, 19 July 2023

OCA — Wed, 19 Jul 2023 06:10:49 GMT

←Older revision		Revision as of 06:10, 19 July 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8b2f is ~~ON HOLD until Paper~~ Publication	+	==SH3-like cell wall binding domain of the GH24 family muramidase from Trichophaea saccata in complex with triglycine==
		+	<StructureSection load='8b2f' size='340' side='right'caption='[[8b2f]], [[Resolution\|resolution]] 1.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8b2f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [https://en.wikipedia.org/wiki/Trichophaea_saccata Trichophaea saccata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8B2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B2F FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.183Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=8b2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2f OCA], [https://pdbe.org/8b2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2f RCSB], [https://www.ebi.ac.uk/pdbsum/8b2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2f ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Muramidases (also known as lysozymes) hydrolyse the peptidoglycan component of the bacterial cell wall and are found in many glycoside hydrolase (GH) families. Similar to other glycoside hydrolases, muramidases sometimes have noncatalytic domains that facilitate their interaction with the substrate. Here, the identification, characterization and X-ray structure of a novel fungal GH24 muramidase from Trichophaea saccata is first described, in which an SH3-like cell-wall-binding domain (CWBD) was identified by structure comparison in addition to its catalytic domain. Further, a complex between a triglycine peptide and the CWBD from T. saccata is presented that shows a possible anchor point of the peptidoglycan on the CWBD. A ;domain-walking' approach, searching for other sequences with a domain of unknown function appended to the CWBD, was then used to identify a group of fungal muramidases that also contain homologous SH3-like cell-wall-binding modules, the catalytic domains of which define a new GH family. The properties of some representative members of this family are described as well as X-ray structures of the independent catalytic and SH3-like domains of the Kionochaeta sp., Thermothielavioides terrestris and Penicillium virgatum enzymes. This work confirms the power of the module-walking approach, extends the library of known GH families and adds a new noncatalytic module to the muramidase arsenal.

-	~~Authors:~~ Moroz~~, O.V.~~, Blagova, E., Lebedev~~, A.A.~~, Skov~~, L.K.~~, Pache~~, R.A.~~, Schnorr~~, K.M.~~, Kiemer, L., Nymand-Grarup, S., Ming, L., Ye, L., Klausen, M., Cohn~~, M.T.~~, Schmidt~~, E.G.W.~~, Davies, G.J.~~, Wilson, K~~.S.	+	Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases.,Moroz OV, Blagova E, Lebedev AA, Skov LK, Pache RA, Schnorr KM, Kiemer L, Friis EP, Nymand-Grarup S, Ming L, Ye L, Klausen M, Cohn MT, Schmidt EGW, Davies GJ, Wilson KS Acta Crystallogr D Struct Biol. 2023 Aug 1. doi: 10.1107/S2059798323005004. PMID:37428847<ref>PMID:37428847</ref>

-	~~Description: SH3-like cell wall binding domain~~ of the ~~GH24 family muramidase from Trichophaea saccata in complex with triglycine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Kiemer, L~~]]	+	<div class="pdbe-citations 8b2f" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Nymand-Grarup, S~~]]	+	== References ==
-	[[Category: ~~Ming, L~~]]	+	<references/>
-	[[Category: ~~Schnorr, K.M~~]]	+	__TOC__
-	[[Category: ~~Lebedev, A.A~~]]	+	</StructureSection>
-	[[Category: ~~Wilson, K.S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ye, L~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Davies, G.J~~]]	+	[[Category: Trichophaea saccata]]
-	[[Category: ~~Klausen, M~~]]	+	[[Category: Blagova E]]
-	[[Category: ~~Skov, L.K~~]]	+	[[Category: Cohn MT]]
-	[[Category: ~~Moroz, O.V~~]]	+	[[Category: Davies GJ]]
-	[[Category: Schmidt~~, E.G.W~~]]	+	[[Category: Kiemer L]]
-	[[Category: ~~Pache, R.A~~]]	+	[[Category: Klausen M]]
-	[[Category: ~~Blagova, E~~]]	+	[[Category: Lebedev AA]]
-	[[Category: ~~Cohn, M.T~~]]	+	[[Category: Ming L]]
		+	[[Category: Moroz OV]]
		+	[[Category: Nymand-Grarup S]]
		+	[[Category: Pache RA]]
		+	[[Category: Schmidt EGW]]
		+	[[Category: Schnorr KM]]
		+	[[Category: Skov LK]]
		+	[[Category: Wilson KS]]
		+	[[Category: Ye L]]

OCA at 03:48, 26 October 2022

OCA — Wed, 26 Oct 2022 03:48:17 GMT

←Older revision		Revision as of 03:48, 26 October 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8b2f is ON HOLD	+	The entry 8b2f is ON HOLD until Paper Publication

	Authors: Moroz, O.V., Blagova, E., Lebedev, A.A., Skov, L.K., Pache, R.A., Schnorr, K.M., Kiemer, L., Nymand-Grarup, S., Ming, L., Ye, L., Klausen, M., Cohn, M.T., Schmidt, E.G.W., Davies, G.J., Wilson, K.S.		Authors: Moroz, O.V., Blagova, E., Lebedev, A.A., Skov, L.K., Pache, R.A., Schnorr, K.M., Kiemer, L., Nymand-Grarup, S., Ming, L., Ye, L., Klausen, M., Cohn, M.T., Schmidt, E.G.W., Davies, G.J., Wilson, K.S.

OCA: Protected "8b2f" [edit=sysop:move=sysop]

OCA — Wed, 21 Sep 2022 06:31:26 GMT

Protected "8b2f" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:31, 21 September 2022

OCA: New page: '''Unreleased structure''' The entry 8b2f is ON HOLD Authors: Moroz, O.V., Blagova, E., Lebedev, A.A., Skov, L.K., Pache, R.A., Schnorr, K.M., Kiemer, L., Nymand-Grarup, S., Ming, L., Y...

OCA — Wed, 21 Sep 2022 06:31:25 GMT

New page: '''Unreleased structure''' The entry 8b2f is ON HOLD Authors: Moroz, O.V., Blagova, E., Lebedev, A.A., Skov, L.K., Pache, R.A., Schnorr, K.M., Kiemer, L., Nymand-Grarup, S., Ming, L., Y...

New page

'''Unreleased structure'''

The entry 8b2f is ON HOLD

Authors: Moroz, O.V., Blagova, E., Lebedev, A.A., Skov, L.K., Pache, R.A., Schnorr, K.M., Kiemer, L., Nymand-Grarup, S., Ming, L., Ye, L., Klausen, M., Cohn, M.T., Schmidt, E.G.W., Davies, G.J., Wilson, K.S.

Description: SH3-like cell wall binding domain of the GH24 family muramidase from Trichophaea saccata in complex with triglycine
[[Category: Unreleased Structures]]
[[Category: Kiemer, L]]
[[Category: Nymand-Grarup, S]]
[[Category: Ming, L]]
[[Category: Schnorr, K.M]]
[[Category: Lebedev, A.A]]
[[Category: Wilson, K.S]]
[[Category: Ye, L]]
[[Category: Davies, G.J]]
[[Category: Klausen, M]]
[[Category: Skov, L.K]]
[[Category: Moroz, O.V]]
[[Category: Schmidt, E.G.W]]
[[Category: Pache, R.A]]
[[Category: Blagova, E]]
[[Category: Cohn, M.T]]