5txi - Revision history

OCA at 13:15, 4 October 2023

OCA — Wed, 04 Oct 2023 13:15:26 GMT

←Older revision		Revision as of 13:15, 4 October 2023
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	<StructureSection load='5txi' size='340' side='right'caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5txi' size='340' side='right'caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TXI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RB6:(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-~~pyrrolidin~~-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>RB6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tw4\|5tw4]], [[5tw8\|5tw8]], [[5tx9\|5tx9]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RB6:(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr+rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>RB6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5txi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txi OCA], [~~http~~://pdbe.org/5txi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5txi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5txi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5txi 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=5txi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txi OCA], [https://pdbe.org/5txi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5txi RCSB], [https://www.ebi.ac.uk/pdbsum/5txi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5txi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2G2X6_STAA8 Q2G2X6_STAA8] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.[ARBA:ARBA00003217]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Alexander, J A.N~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Strynadka, N C.J~~]]	+	[[Category: Alexander JAN]]
-	[[Category: ~~Antibiotic]]~~	+	[[Category: Strynadka NCJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase - antibiotic complex~~]]	+

OCA at 08:20, 8 January 2020

OCA — Wed, 08 Jan 2020 08:20:01 GMT

←Older revision		Revision as of 08:20, 8 January 2020
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	==Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with ceftobiprole==		==Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with ceftobiprole==
-	<StructureSection load='5txi' size='340' side='right' caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5txi' size='340' side='right'caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXI FirstGlance]. <br>
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Penicillin-binding protein\|Penicillin-binding protein]]	+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Alexander, J A.N]]		[[Category: Alexander, J A.N]]
	[[Category: Strynadka, N C.J]]		[[Category: Strynadka, N C.J]]

OCA at 20:45, 2 December 2018

OCA — Sun, 02 Dec 2018 20:45:58 GMT

←Older revision		Revision as of 20:45, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5txi' size='340' side='right' caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5txi' size='340' side='right' caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RB6:(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyrrolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>RB6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RB6:(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyrrolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>RB6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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">[[5tw4\|5tw4]], [[5tw8\|5tw8]], [[5tx9\|5tx9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tw4\|5tw4]], [[5tw8\|5tw8]], [[5tx9\|5tx9]]</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=5txi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txi OCA], [http://pdbe.org/5txi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txi RCSB], [http://www.ebi.ac.uk/pdbsum/5txi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txi ProSAT]</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=5txi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txi OCA], [http://pdbe.org/5txi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txi RCSB], [http://www.ebi.ac.uk/pdbsum/5txi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txi ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methicillin-resistant Staphylococcus aureus (MRSA) causes serious community-acquired and nosocomial infections worldwide. MRSA strains are resistant to a variety of antibiotics, including the classic penicillin and cephalosporin classes of beta-lactams, making them intractable to treatment. Although beta-lactam resistance in MRSA has been ascribed to the acquisition and activity of penicillin-binding protein 2a (PBP2a, encoded by mecA), it has recently been observed that resistance can also be mediated by penicillin-binding protein 4 (PBP4). Previously, we have shown that broad-spectrum beta-lactam resistance can arise following serial passaging of a mecA-negative COL strain of S. aureus, creating the CRB strain. This strain has two missense mutations in pbp4 and a mutation in the pbp4 promoter, both of which play an instrumental role in beta-lactam resistance. To better understand PBP4's role in resistance, here we have characterized its kinetics and structure with clinically relevant beta-lactam antibiotics. We present the first crystallographic PBP4 structures of apo and acyl-enzyme intermediate forms complexed with three late-generation beta-lactam antibiotics: ceftobiprole, ceftaroline, and nafcillin. In parallel, we characterized the structural and kinetic effects of the PBP4 mutations present in the CRB strain. Localized within the transpeptidase active-site cleft, the two substitutions appear to have different effects depending on the drug. With ceftobiprole, the missense mutations impaired the KM value 150-fold, decreasing the proportion of inhibited PBP4. However, ceftaroline resistance appeared to be mediated by other factors, possibly including mutation of the pbp4 promoter. Our findings provide evidence that S. aureus CRB has at least two PBP4-mediated resistance mechanisms.
		+
		+	Structural and kinetic analysis of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance in Staphylococcus aureus.,Alexander JAN, Chatterjee SS, Hamilton SM, Eltis LD, Chambers HF, Strynadka NCJ J Biol Chem. 2018 Oct 26. pii: RA118.004952. doi: 10.1074/jbc.RA118.004952. PMID:30366985<ref>PMID:30366985</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5txi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein\|Penicillin-binding protein]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:24, 16 May 2018

OCA — Wed, 16 May 2018 05:24:10 GMT

←Older revision		Revision as of 05:24, 16 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5txi is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with ceftobiprole==
-		+	<StructureSection load='5txi' size='340' side='right' caption='[[5txi]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5txi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TXI FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RB6:(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyrrolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>RB6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tw4\|5tw4]], [[5tw8\|5tw8]], [[5tx9\|5tx9]]</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=5txi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5txi OCA], [http://pdbe.org/5txi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5txi RCSB], [http://www.ebi.ac.uk/pdbsum/5txi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5txi ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alexander, J A.N]]
		+	[[Category: Strynadka, N C.J]]
		+	[[Category: Antibiotic]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase - antibiotic complex]]

OCA at 21:24, 25 January 2017

OCA — Wed, 25 Jan 2017 21:24:43 GMT

←Older revision		Revision as of 21:24, 25 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Fri, 09 Dec 2016 18:01:16 GMT

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

←Older revision

Revision as of 18:01, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5txi is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 18:01:15 GMT

New page: '''Unreleased structure''' The entry 5txi is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5txi is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]