6dja - Revision history

OCA at 06:07, 11 October 2023

2023-10-11T06:07:47Z

←Older revision		Revision as of 06:07, 11 October 2023
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	<StructureSection load='6dja' size='340' side='right'caption='[[6dja]], [[Resolution\|resolution]] 2.48Å' scene=''>		<StructureSection load='6dja' size='340' side='right'caption='[[6dja]], [[Resolution\|resolution]] 2.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dja]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_14579 Atcc 14579~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DJA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dja]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DJA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 2.48Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6]~~ </~~span~~></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='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=6dja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dja OCA], [~~http~~://pdbe.org/6dja PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dja RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dja PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dja 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=6dja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dja OCA], [https://pdbe.org/6dja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dja RCSB], [https://www.ebi.ac.uk/pdbsum/6dja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dja ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BLAB_BACCE BLAB_BACCE]] Confers resistance to the different beta-lactams antibiotics (penicillin, cephalosporin and carbapenem) via the hydrolysis of the beta-lactam ring. Benzylpenicillin is a better substrate than cephalosporin C and ampicillin (PubMed:3131315, PubMed:2501295).<ref>PMID:1904717</ref> <ref>PMID:2501295</ref> <ref>PMID:3131315</ref>	+	[https://www.uniprot.org/uniprot/BLAB_BACCE BLAB_BACCE] Confers resistance to the different beta-lactams antibiotics (penicillin, cephalosporin and carbapenem) via the hydrolysis of the beta-lactam ring. Benzylpenicillin is a better substrate than cephalosporin C and ampicillin (PubMed:3131315, PubMed:2501295).<ref>PMID:1904717</ref> <ref>PMID:2501295</ref> <ref>PMID:3131315</ref>
	<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 6dja" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dja" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 14579]]~~	+	[[Category: Bacillus cereus]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bui~~, A A~~]]	+	[[Category: Bui AA]]
-	[[Category: Khan~~, N H~~]]	+	[[Category: Khan NH]]
-	[[Category: Shaw~~, R W~~]]	+	[[Category: Shaw RW]]
-	[[Category: Sutton~~, R B]]~~	+	[[Category: Sutton RB]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lactamase]]~~	+
-	~~[[Category: Zinc~~]]	+

OCA at 17:54, 11 December 2019

2019-12-11T17:54:46Z

←Older revision		Revision as of 17:54, 11 December 2019
Line 3:		Line 3:
	<StructureSection load='6dja' size='340' side='right'caption='[[6dja]], [[Resolution\|resolution]] 2.48Å' scene=''>		<StructureSection load='6dja' size='340' side='right'caption='[[6dja]], [[Resolution\|resolution]] 2.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dja]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dja]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DJA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BLAB_BACCE BLAB_BACCE]] Confers resistance to the different beta-lactams antibiotics (penicillin, cephalosporin and carbapenem) via the hydrolysis of the beta-lactam ring. Benzylpenicillin is a better substrate than cephalosporin C and ampicillin (PubMed:3131315, PubMed:2501295).<ref>PMID:1904717</ref> <ref>PMID:2501295</ref> <ref>PMID:3131315</ref>		[[http://www.uniprot.org/uniprot/BLAB_BACCE BLAB_BACCE]] Confers resistance to the different beta-lactams antibiotics (penicillin, cephalosporin and carbapenem) via the hydrolysis of the beta-lactam ring. Benzylpenicillin is a better substrate than cephalosporin C and ampicillin (PubMed:3131315, PubMed:2501295).<ref>PMID:1904717</ref> <ref>PMID:2501295</ref> <ref>PMID:3131315</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hydrolysis of beta-lactam antibiotics by beta-lactamase enzymes is the most prominent antibiotic resistance mechanism for many pathogenic bacteria. Out of this broad class of enzymes, metallo-beta-lactamases are of special clinical interest because of their broad substrate specificities. Several in vitro inhibitors for various metallo-beta-lactamases have been reported with no clinical efficacy. Previously, we described a 10-nucleotide single stranded DNA aptamer (10-mer) that inhibits Bacillus cereus 5/B/6 metallo-beta-lactamase very effectively. Here, we find that the aptamer shows uncompetitive inhibition of Bacillus cereus 5/B/6 metallo-beta-lactamase during cefuroxime hydrolysis. To understand the mechanism of inhibition, we report a 2.5 A resolution X-ray crystal structure and solution-state NMR analysis of the free enzyme. Chemical shift perturbations were observed in the HSQC spectra for several residues upon titrating with increasing concentrations of the 10-mer. In the X-ray crystal structure, these residues are distal to the active site, suggesting an allosteric mechanism for the aptamer inhibition of the enzyme. HADDOCK molecular docking simulations suggest that the 10-mer docks 26 A from the active site. We then mutated the three lysine residues in the basic binding patch to glutamine and measured the catalytic activity and inhibition by the 10-mer. No significant inhibition of these mutants was observed by the 10-mer as compared to wild type. Interestingly, mutation of Lys50 (Lys78; according to standard MBL numbering system) resulted in reduced enzymatic activity relative to wild type in the absence of inhibitor, further highlighting an allosteric mechanism for inhibition.
		+
		+	A DNA aptamer reveals an allosteric site for inhibition in metallo-beta-lactamases.,Khan NH, Bui AA, Xiao Y, Sutton RB, Shaw RW, Wylie BJ, Latham MP PLoS One. 2019 Apr 22;14(4):e0214440. doi: 10.1371/journal.pone.0214440., eCollection 2019. PMID:31009467<ref>PMID:31009467</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dja" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 14579]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:04, 29 May 2019

2019-05-29T06:04:48Z

←Older revision		Revision as of 06:04, 29 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dja is ~~ON HOLD until Paper Publication~~	+	==ZN-DEPENDENT 5/B/6 METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS==
-		+	<StructureSection load='6dja' size='340' side='right'caption='[[6dja]], [[Resolution\|resolution]] 2.48Å' scene=''>
-	~~Authors~~: ~~Bui~~, A.A., ~~Khan, N~~.H., ~~Shaw~~, R.W., ~~Sutton~~, R.B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dja]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DJA FirstGlance]. <br>
-	~~Description~~: ~~ZN-DEPENDENT 5~~/B/~~6 METALLO~~-~~BETA~~-~~LACTAMASE FROM BACILLUS CEREUS~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
-	[[Category: ~~Sutton, R.B~~]]	+	<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=6dja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dja OCA], [http://pdbe.org/6dja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dja RCSB], [http://www.ebi.ac.uk/pdbsum/6dja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dja ProSAT]</span></td></tr>
-	[[Category: Bui, A.A]]	+	</table>
-	[[Category: Khan, N.H]]	+	== Function ==
-	[[Category: Shaw, R.W]]	+	[[http://www.uniprot.org/uniprot/BLAB_BACCE BLAB_BACCE]] Confers resistance to the different beta-lactams antibiotics (penicillin, cephalosporin and carbapenem) via the hydrolysis of the beta-lactam ring. Benzylpenicillin is a better substrate than cephalosporin C and ampicillin (PubMed:3131315, PubMed:2501295).<ref>PMID:1904717</ref> <ref>PMID:2501295</ref> <ref>PMID:3131315</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
		+	[[Category: Bui, A A]]
		+	[[Category: Khan, N H]]
		+	[[Category: Shaw, R W]]
		+	[[Category: Sutton, R B]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lactamase]]
		+	[[Category: Zinc]]

OCA at 05:20, 18 July 2018

2018-07-18T05:20:31Z

←Older revision		Revision as of 05:20, 18 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dja is ON HOLD	+	The entry 6dja is ON HOLD until Paper Publication

	Authors: Bui, A.A., Khan, N.H., Shaw, R.W., Sutton, R.B.		Authors: Bui, A.A., Khan, N.H., Shaw, R.W., Sutton, R.B.

OCA: Protected "6dja" [edit=sysop:move=sysop]

2018-05-30T04:13:13Z

Protected "6dja" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:13, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dja is ON HOLD Authors: Bui, A.A., Khan, N.H., Shaw, R.W., Sutton, R.B. Description: ZN-DEPENDENT 5/B/6 METALLO-BETA-LACTAMASE FROM BACILLUS CEREU...

2018-05-30T04:13:11Z

New page: '''Unreleased structure''' The entry 6dja is ON HOLD Authors: Bui, A.A., Khan, N.H., Shaw, R.W., Sutton, R.B. Description: ZN-DEPENDENT 5/B/6 METALLO-BETA-LACTAMASE FROM BACILLUS CEREU...

New page

'''Unreleased structure'''

The entry 6dja is ON HOLD

Authors: Bui, A.A., Khan, N.H., Shaw, R.W., Sutton, R.B.

Description: ZN-DEPENDENT 5/B/6 METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS
[[Category: Unreleased Structures]]
[[Category: Sutton, R.B]]
[[Category: Bui, A.A]]
[[Category: Khan, N.H]]
[[Category: Shaw, R.W]]