8b2g - Revision history

OCA at 08:15, 7 February 2024

2024-02-07T08:15:42Z

←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=8b2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2g OCA], [https://pdbe.org/8b2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2g RCSB], [https://www.ebi.ac.uk/pdbsum/8b2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2g 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=8b2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2g OCA], [https://pdbe.org/8b2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2g RCSB], [https://www.ebi.ac.uk/pdbsum/8b2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2g 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 8b2g" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:10, 19 July 2023

2023-07-19T06:10:49Z

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

-	~~The entry~~ 8b2g is ~~ON HOLD until Paper~~ Publication	+	==SH3-like domain from Penicillium virgatum muramidase==
		+	<StructureSection load='8b2g' size='340' side='right'caption='[[8b2g]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8b2g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_virgatum Penicillium virgatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8B2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B2G 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]] 1.5Å</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=8b2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b2g OCA], [https://pdbe.org/8b2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b2g RCSB], [https://www.ebi.ac.uk/pdbsum/8b2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b2g 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 domain from Penicillium virgatum muramidase~~	+	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 8b2g" 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: Penicillium virgatum]]
-	[[Category: ~~Davies, G.J~~]]	+	[[Category: Blagova E]]
-	[[Category: ~~Klausen, M~~]]	+	[[Category: Cohn MT]]
-	[[Category: ~~Skov, L.K~~]]	+	[[Category: Davies GJ]]
-	[[Category: ~~Moroz, O.V~~]]	+	[[Category: Kiemer L]]
-	[[Category: Schmidt~~, E.G.W~~]]	+	[[Category: Klausen M]]
-	[[Category: ~~Pache, R.A~~]]	+	[[Category: Lebedev AA]]
-	[[Category: ~~Blagova, E~~]]	+	[[Category: Ming L]]
-	[[Category: ~~Cohn, M.T~~]]	+	[[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

2022-10-26T03:48:31Z

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

-	The entry 8b2g is ON HOLD	+	The entry 8b2g 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 "8b2g" [edit=sysop:move=sysop]

2022-09-21T06:31:28Z

Protected "8b2g" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:31, 21 September 2022

OCA: New page: '''Unreleased structure''' The entry 8b2g 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...

2022-09-21T06:31:27Z

New page: '''Unreleased structure''' The entry 8b2g 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 8b2g 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 domain from Penicillium virgatum muramidase
[[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]]