5zhw - Revision history

OCA at 08:56, 22 November 2023

OCA — Wed, 22 Nov 2023 08:56:11 GMT

←Older revision		Revision as of 08:56, 22 November 2023
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	<StructureSection load='5zhw' size='340' side='right'caption='[[5zhw]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='5zhw' size='340' side='right'caption='[[5zhw]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zhw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZHW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zhw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis_V583 Enterococcus faecalis V583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZHW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DAL:D~~-~~ALANINE'>DAL</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2.18Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"~~>~~[[5zhf\|5zhf]]~~</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=5zhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhw OCA], [https://pdbe.org/5zhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zhw RCSB], [https://www.ebi.ac.uk/pdbsum/5zhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhw ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhw OCA], [~~http~~://pdbe.org/5zhw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zhw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zhw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VANY_ENTFA VANY_ENTFA]] Vancomycin-inducible, penicillin-resistant, DD-carboxypeptidase that hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors. Insensitive to beta-lactams.	+	[https://www.uniprot.org/uniprot/VANY_ENTFA VANY_ENTFA] Vancomycin-inducible, penicillin-resistant, DD-carboxypeptidase that hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors. Insensitive to beta-lactams.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterococcus faecalis V583]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Hahn H]]
-	[[Category: Hahn, H]]	+	[[Category: Kim HS]]
-	[[Category: Kim~~, H S]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallopeptidase family m15]]~~	+
-	~~[[Category: Peptidase]]~~	+
-	~~[[Category: Vancomycin resistance~~]]	+

OCA at 21:19, 28 October 2020

OCA — Wed, 28 Oct 2020 21:19:51 GMT

←Older revision		Revision as of 21:19, 28 October 2020
Line 1:		Line 1:

	==VanYB in complex with D-Alanine-D-Alanine==		==VanYB in complex with D-Alanine-D-Alanine==
-	<StructureSection load='5zhw' size='340' side='right' caption='[[5zhw]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='5zhw' size='340' side='right'caption='[[5zhw]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zhw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZHW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zhw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZHW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zhf\|5zhf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zhf\|5zhf]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5zhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhw OCA], [http://pdbe.org/5zhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhw RCSB], [http://www.ebi.ac.uk/pdbsum/5zhw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhw ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhw OCA], [http://pdbe.org/5zhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhw RCSB], [http://www.ebi.ac.uk/pdbsum/5zhw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5zhw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zhw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Hahn, H]]		[[Category: Hahn, H]]

OCA at 10:02, 5 September 2018

OCA — Wed, 05 Sep 2018 10:02:14 GMT

←Older revision		Revision as of 10:02, 5 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zhw is ~~ON HOLD until Paper~~ Publication	+	==VanYB in complex with D-Alanine-D-Alanine==
		+	<StructureSection load='5zhw' size='340' side='right' caption='[[5zhw]], [[Resolution\|resolution]] 2.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zhw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZHW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zhf\|5zhf]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhw OCA], [http://pdbe.org/5zhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhw RCSB], [http://www.ebi.ac.uk/pdbsum/5zhw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VANY_ENTFA VANY_ENTFA]] Vancomycin-inducible, penicillin-resistant, DD-carboxypeptidase that hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors. Insensitive to beta-lactams.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanYB in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala(4)-d-Ala(5) extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanYB manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanYB in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanYB and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanYB. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanYB around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.

-	~~Authors:~~ Kim, H~~.S.~~, ~~Hahn~~, H.	+	Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.,Kim HS, Hahn H, Kim J, Jang DM, Lee JY, Back JM, Im HN, Kim H, Han BW, Suh SW Int J Biol Macromol. 2018 Jul 27;119:335-344. doi:, 10.1016/j.ijbiomac.2018.07.081. PMID:30016658<ref>PMID:30016658</ref>

-	~~Description: VanYB in complex with D~~-~~Alanine~~-~~D-Alanine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Kim, H.S~~]]	+	<div class="pdbe-citations 5zhw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Hahn, H]]		[[Category: Hahn, H]]
		+	[[Category: Kim, H S]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallopeptidase family m15]]
		+	[[Category: Peptidase]]
		+	[[Category: Vancomycin resistance]]

OCA at 05:46, 23 May 2018

OCA — Wed, 23 May 2018 05:46:19 GMT

←Older revision		Revision as of 05:46, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zhw is ON HOLD	+	The entry 5zhw is ON HOLD until Paper Publication

	Authors: Kim, H.S., Hahn, H.		Authors: Kim, H.S., Hahn, H.

OCA: Protected "5zhw" [edit=sysop:move=sysop]

OCA — Wed, 21 Mar 2018 06:01:36 GMT

Protected "5zhw" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:01, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zhw is ON HOLD Authors: Kim, H.S., Hahn, H. Description: VanYB in complex with D-Alanine-D-Alanine Category: Unreleased Structures [[Category:...

OCA — Wed, 21 Mar 2018 06:01:35 GMT

New page: '''Unreleased structure''' The entry 5zhw is ON HOLD Authors: Kim, H.S., Hahn, H. Description: VanYB in complex with D-Alanine-D-Alanine Category: Unreleased Structures [[Category:...

New page

'''Unreleased structure'''

The entry 5zhw is ON HOLD

Authors: Kim, H.S., Hahn, H.

Description: VanYB in complex with D-Alanine-D-Alanine
[[Category: Unreleased Structures]]
[[Category: Kim, H.S]]
[[Category: Hahn, H]]