7bz1 - Revision history

OCA at 15:43, 29 November 2023

OCA — Wed, 29 Nov 2023 15:43:43 GMT

←Older revision		Revision as of 15:43, 29 November 2023
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	<StructureSection load='7bz1' size='340' side='right'caption='[[7bz1]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='7bz1' size='340' side='right'caption='[[7bz1]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7bz1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bz1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[6j4n\|6j4n]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6]~~ </~~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=7bz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz1 OCA], [https://pdbe.org/7bz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz1 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz1 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=7bz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz1 OCA], [https://pdbe.org/7bz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz1 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2U8UYM6_9BACT A0A2U8UYM6_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7bz1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7bz1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kang, L W~~]]	+	[[Category: Uncultured bacterium]]
-	[[Category: ~~Lee, J H~~]]	+	[[Category: Kang LW]]
-	[[Category: ~~Park, Y S~~]]	+	[[Category: Lee JH]]
-	[[Category: ~~Antibiotic]]~~	+	[[Category: Park YS]]
-	~~[[Category: Mbl]]~~	+
-	~~[[Category: Rnase z]]~~	+
-	~~[[Category: Zinc binding motif~~]]	+

OCA at 09:09, 5 May 2021

OCA — Wed, 05 May 2021 09:09:15 GMT

←Older revision		Revision as of 09:09, 5 May 2021
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	==The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.==		==The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.==
-	<StructureSection load='7bz1' size='340' side='right'caption='[[7bz1]]' scene=''>	+	<StructureSection load='7bz1' size='340' side='right'caption='[[7bz1]], [[Resolution\|resolution]] 2.45Å' 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=7BZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bz1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ1 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=7bz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz1 OCA], [https://pdbe.org/7bz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz1 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz1 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=ZN:ZINC+ION'>ZN</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;'>[[6j4n\|6j4n]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=7bz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz1 OCA], [https://pdbe.org/7bz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz1 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although beta-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to beta-lactam antibiotics by producing beta-lactamases. Among beta-lactamases, metallo-beta-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes beta-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and beta-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.
		+
		+	Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants.,Park YS, Kim TY, Park H, Lee JH, Nguyen DQ, Hong MK, Lee SH, Kang LW Int J Mol Sci. 2020 Jul 12;21(14). pii: ijms21144926. doi: 10.3390/ijms21144926. PMID:32664695<ref>PMID:32664695</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bz1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kang LW]]	+	[[Category: Kang, L W]]
-	[[Category: Lee JH]]	+	[[Category: Lee, J H]]
-	[[Category: Park YS]]	+	[[Category: Park, Y S]]
		+	[[Category: Antibiotic]]
		+	[[Category: Mbl]]
		+	[[Category: Rnase z]]
		+	[[Category: Zinc binding motif]]

OCA at 05:19, 28 April 2021

OCA — Wed, 28 Apr 2021 05:19:51 GMT

←Older revision		Revision as of 05:19, 28 April 2021
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-	'''Unreleased structure'''

-	~~The entry 7bz1 is ON HOLD until Paper Publication~~	+	==The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.==
-		+	<StructureSection load='7bz1' size='340' side='right'caption='[[7bz1]]' scene=''>
-	~~Authors: Park, Y.S., Kang, L.W., Lee, J.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ1 FirstGlance]. <br>
-	~~Description:~~ The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.	+	</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=7bz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz1 OCA], [https://pdbe.org/7bz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz1 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Park, Y.S~~]]	+	__TOC__
-	[[Category: Lee~~, J.H~~]]	+	</StructureSection>
-	[[Category: ~~Kang, L.W~~]]	+	[[Category: Large Structures]]
		+	[[Category: Kang LW]]
		+	[[Category: Lee JH]]
		+	[[Category: Park YS]]

OCA at 05:55, 21 April 2021

OCA — Wed, 21 Apr 2021 05:55:49 GMT

←Older revision		Revision as of 05:55, 21 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7bz1 is ON HOLD	+	The entry 7bz1 is ON HOLD until Paper Publication

	Authors: Park, Y.S., Kang, L.W., Lee, J.H.		Authors: Park, Y.S., Kang, L.W., Lee, J.H.
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	Description: The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.		Description: The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Park, Y.S]]
	[[Category: Lee, J.H]]		[[Category: Lee, J.H]]
	[[Category: Kang, L.W]]		[[Category: Kang, L.W]]
-	[[Category: Park, Y.S]]

OCA: Protected "7bz1" [edit=sysop:move=sysop]

OCA — Wed, 06 May 2020 04:53:35 GMT

Protected "7bz1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:53, 6 May 2020

OCA: New page: '''Unreleased structure''' The entry 7bz1 is ON HOLD Authors: Park, Y.S., Kang, L.W., Lee, J.H. Description: The mutant variant of PNGM-1. H96 was substituted for alanine to study meta...

OCA — Wed, 06 May 2020 04:53:32 GMT

New page: '''Unreleased structure''' The entry 7bz1 is ON HOLD Authors: Park, Y.S., Kang, L.W., Lee, J.H. Description: The mutant variant of PNGM-1. H96 was substituted for alanine to study meta...

New page

'''Unreleased structure'''

The entry 7bz1 is ON HOLD

Authors: Park, Y.S., Kang, L.W., Lee, J.H.

Description: The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.
[[Category: Unreleased Structures]]
[[Category: Lee, J.H]]
[[Category: Kang, L.W]]
[[Category: Park, Y.S]]