8f5d - Revision history

OCA at 07:27, 3 April 2024

OCA — Wed, 03 Apr 2024 07:27:04 GMT

←Older revision		Revision as of 07:27, 3 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8f5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_pertussis_18323 Bordetella pertussis 18323]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8F5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8F5D FirstGlance]. <br>		<table><tr><td colspan='2'>[[8f5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_pertussis_18323 Bordetella pertussis 18323]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8F5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8F5D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.56Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8f5d OCA], [https://pdbe.org/8f5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8f5d RCSB], [https://www.ebi.ac.uk/pdbsum/8f5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8f5d 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=8f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8f5d OCA], [https://pdbe.org/8f5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8f5d RCSB], [https://www.ebi.ac.uk/pdbsum/8f5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8f5d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A0T7CQ89_BORP1 A0A0T7CQ89_BORP1] Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.[HAMAP-Rule:MF_00208] Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.[HAMAP-Rule:MF_02019][RuleBase:RU004136]		[https://www.uniprot.org/uniprot/A0A0T7CQ89_BORP1 A0A0T7CQ89_BORP1] Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.[HAMAP-Rule:MF_00208] Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.[HAMAP-Rule:MF_02019][RuleBase:RU004136]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Peptidoglycan (PG) is a central component of the bacterial cell wall, and the disruption of its biosynthetic pathway has been a successful antibacterial strategy for decades. PG biosynthesis is initiated in the cytoplasm through sequential reactions catalyzed by Mur enzymes that have been suggested to associate into a multimembered complex. This idea is supported by the observation that in many eubacteria, mur genes are present in a single operon within the well conserved dcw cluster, and in some cases, pairs of mur genes are fused to encode a single, chimeric polypeptide. We performed a vast genomic analysis using >140 bacterial genomes and mapped Mur chimeras in numerous phyla, with Proteobacteria carrying the highest number. MurE-MurF, the most prevalent chimera, exists in forms that are either directly associated or separated by a linker. The crystal structure of the MurE-MurF chimera from Bordetella pertussis reveals a head-to-tail, elongated architecture supported by an interconnecting hydrophobic patch that stabilizes the positions of the two proteins. Fluorescence polarization assays reveal that MurE-MurF interacts with other Mur ligases via its central domains with K(D)s in the high nanomolar range, backing the existence of a Mur complex in the cytoplasm. These data support the idea of stronger evolutionary constraints on gene order when encoded proteins are intended for association, establish a link between Mur ligase interaction, complex assembly and genome evolution, and shed light on regulatory mechanisms of protein expression and stability in pathways of critical importance for bacterial survival.
-
-	Architecture and genomic arrangement of the MurE-MurF bacterial cell wall biosynthesis complex.,Shirakawa KT, Sala FA, Miyachiro MM, Job V, Trindade DM, Dessen A Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2219540120. doi: , 10.1073/pnas.2219540120. Epub 2023 May 15. PMID:37186837<ref>PMID:37186837</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8f5d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:40, 7 June 2023

OCA — Wed, 07 Jun 2023 05:40:11 GMT

←Older revision		Revision as of 05:40, 7 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8f5d is ~~ON HOLD~~ ~~until 2024~~-11-14	+	==Architecture of the MurE-MurF ligase bacterial cell wall biosynthesis complex==
		+	<StructureSection load='8f5d' size='340' side='right'caption='[[8f5d]], [[Resolution\|resolution]] 2.56Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8f5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_pertussis_18323 Bordetella pertussis 18323]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8F5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8F5D FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8f5d OCA], [https://pdbe.org/8f5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8f5d RCSB], [https://www.ebi.ac.uk/pdbsum/8f5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8f5d ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0T7CQ89_BORP1 A0A0T7CQ89_BORP1] Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.[HAMAP-Rule:MF_00208] Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.[HAMAP-Rule:MF_02019][RuleBase:RU004136]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan (PG) is a central component of the bacterial cell wall, and the disruption of its biosynthetic pathway has been a successful antibacterial strategy for decades. PG biosynthesis is initiated in the cytoplasm through sequential reactions catalyzed by Mur enzymes that have been suggested to associate into a multimembered complex. This idea is supported by the observation that in many eubacteria, mur genes are present in a single operon within the well conserved dcw cluster, and in some cases, pairs of mur genes are fused to encode a single, chimeric polypeptide. We performed a vast genomic analysis using >140 bacterial genomes and mapped Mur chimeras in numerous phyla, with Proteobacteria carrying the highest number. MurE-MurF, the most prevalent chimera, exists in forms that are either directly associated or separated by a linker. The crystal structure of the MurE-MurF chimera from Bordetella pertussis reveals a head-to-tail, elongated architecture supported by an interconnecting hydrophobic patch that stabilizes the positions of the two proteins. Fluorescence polarization assays reveal that MurE-MurF interacts with other Mur ligases via its central domains with K(D)s in the high nanomolar range, backing the existence of a Mur complex in the cytoplasm. These data support the idea of stronger evolutionary constraints on gene order when encoded proteins are intended for association, establish a link between Mur ligase interaction, complex assembly and genome evolution, and shed light on regulatory mechanisms of protein expression and stability in pathways of critical importance for bacterial survival.

-	~~Authors~~:	+	Architecture and genomic arrangement of the MurE-MurF bacterial cell wall biosynthesis complex.,Shirakawa KT, Sala FA, Miyachiro MM, Job V, Trindade DM, Dessen A Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2219540120. doi: , 10.1073/pnas.2219540120. Epub 2023 May 15. PMID:37186837<ref>PMID:37186837</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8f5d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bordetella pertussis 18323]]
		+	[[Category: Large Structures]]
		+	[[Category: Dessen A]]
		+	[[Category: Job V]]
		+	[[Category: Miyachiro MM]]
		+	[[Category: Sala FA]]
		+	[[Category: Shirakawa KT]]
		+	[[Category: Trindade DM]]

OCA at 07:37, 14 December 2022

OCA — Wed, 14 Dec 2022 07:37:41 GMT

←Older revision		Revision as of 07:37, 14 December 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8f5d is ON HOLD	+	The entry 8f5d is ON HOLD until 2024-11-14

	Authors:		Authors:

OCA: Protected "8f5d" [edit=sysop:move=sysop]

OCA — Thu, 24 Nov 2022 08:13:21 GMT

Protected "8f5d" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:13, 24 November 2022

OCA: New page: '''Unreleased structure''' The entry 8f5d is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 24 Nov 2022 08:13:20 GMT

New page: '''Unreleased structure''' The entry 8f5d is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8f5d is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]