8sy9 - Revision history

OCA at 11:23, 14 March 2024

OCA — Thu, 14 Mar 2024 11:23:24 GMT

←Older revision		Revision as of 11:23, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q72KY0_THET2 Q72KY0_THET2]		[https://www.uniprot.org/uniprot/Q72KY0_THET2 Q72KY0_THET2]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, was first identified approximately 40 years ago in the O-antigen of Pseudomonas aeruginosa O:3,a,d. Since then, it has been observed on the O-antigens of various pathogenic Gram-negative bacteria including Bordetella pertussis, Escherichia albertii, and Pseudomonas mediterranea. Previous studies have established that five enzymes are required for its biosynthesis beginning with uridine dinucleotide (UDP)-N-acetyl-d-glucosamine (UDP-GlcNAc). The final step in the pathway is catalyzed by a 2-epimerase, which utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate. Curious as to whether this biochemical pathway is found in extreme thermophiles, we examined the published genome sequence for Thermus thermophilus HB27 and identified five ORFs that could possibly encode for the required enzymes. The focus of this investigation is on the ORF WP_011172736, which we demonstrate encodes for a 2-epimerase. For this investigation, ten high resolution X-ray crystallographic structures were determined to resolutions of 2.3 A or higher. The models have revealed the manner in which the 2-epimerase anchors its UDP-sugar substrate as well as its UDP-sugar product into the active site. In addition, this study reveals for the first time the manner in which any sugar 2-epimerase can simultaneously bind UDP-sugars in both the active site and the allosteric binding region. We have also demonstrated that the T. thermophilus enzyme is allosterically regulated by UDP-GlcNAc. Whereas the sugar 2-epimerases that function on UDP-GlcNAc have been the focus of past biochemical and structural analyses, this is the first detailed investigation of a 2-epimerase that specifically utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate.
-
-	Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.,Thoden JB, McKnight JO, Kroft CW, Jast JDT, Holden HM J Biol Chem. 2023 Sep 3;299(10):105200. doi: 10.1016/j.jbc.2023.105200. PMID:37660908<ref>PMID:37660908</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8sy9" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:42, 18 October 2023

OCA — Wed, 18 Oct 2023 17:42:27 GMT

←Older revision		Revision as of 17:42, 18 October 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8sy9 is ~~ON HOLD until Paper~~ Publication	+	==X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid, UDP-N-acetylglucosamine and UDP at pH 7==
		+	<StructureSection load='8sy9' size='340' side='right'caption='[[8sy9]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8sy9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SY9 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MJL:(2~{S},3~{S},4~{R},5~{R},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic+acid'>MJL</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=8sy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8sy9 OCA], [https://pdbe.org/8sy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8sy9 RCSB], [https://www.ebi.ac.uk/pdbsum/8sy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8sy9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72KY0_THET2 Q72KY0_THET2]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, was first identified approximately 40 years ago in the O-antigen of Pseudomonas aeruginosa O:3,a,d. Since then, it has been observed on the O-antigens of various pathogenic Gram-negative bacteria including Bordetella pertussis, Escherichia albertii, and Pseudomonas mediterranea. Previous studies have established that five enzymes are required for its biosynthesis beginning with uridine dinucleotide (UDP)-N-acetyl-d-glucosamine (UDP-GlcNAc). The final step in the pathway is catalyzed by a 2-epimerase, which utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate. Curious as to whether this biochemical pathway is found in extreme thermophiles, we examined the published genome sequence for Thermus thermophilus HB27 and identified five ORFs that could possibly encode for the required enzymes. The focus of this investigation is on the ORF WP_011172736, which we demonstrate encodes for a 2-epimerase. For this investigation, ten high resolution X-ray crystallographic structures were determined to resolutions of 2.3 A or higher. The models have revealed the manner in which the 2-epimerase anchors its UDP-sugar substrate as well as its UDP-sugar product into the active site. In addition, this study reveals for the first time the manner in which any sugar 2-epimerase can simultaneously bind UDP-sugars in both the active site and the allosteric binding region. We have also demonstrated that the T. thermophilus enzyme is allosterically regulated by UDP-GlcNAc. Whereas the sugar 2-epimerases that function on UDP-GlcNAc have been the focus of past biochemical and structural analyses, this is the first detailed investigation of a 2-epimerase that specifically utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate.

-	~~Authors:~~ Thoden, J.B.~~, Holden, H~~.M.	+	Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.,Thoden JB, McKnight JO, Kroft CW, Jast JDT, Holden HM J Biol Chem. 2023 Sep 3;299(10):105200. doi: 10.1016/j.jbc.2023.105200. PMID:37660908<ref>PMID:37660908</ref>

-	~~Description: X-ray crystal structure~~ of ~~UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in~~ the ~~presence~~ of ~~UDP~~-~~2,3~~-~~diacetamido-2,3-dideoxy-glucuronic acid, UDP-N-acetylglucosamine and UDP at pH 7~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Thoden, J.B~~]]	+	<div class="pdbe-citations 8sy9" style="background-color:#fffaf0;"></div>
-	[[Category: Holden~~, H.M~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Thermus thermophilus HB27]]
		+	[[Category: Holden HM]]
		+	[[Category: Thoden JB]]

OCA at 04:27, 7 June 2023

OCA — Wed, 07 Jun 2023 04:27:32 GMT

←Older revision		Revision as of 04:27, 7 June 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8sy9 is ON HOLD	+	The entry 8sy9 is ON HOLD until Paper Publication

	Authors: Thoden, J.B., Holden, H.M.		Authors: Thoden, J.B., Holden, H.M.

-	Description: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid, UDP-N-~~acetylglucosamoine~~ and UDP at pH 7	+	Description: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid, UDP-N-acetylglucosamine and UDP at pH 7
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Thoden, J.B]]		[[Category: Thoden, J.B]]
	[[Category: Holden, H.M]]		[[Category: Holden, H.M]]

OCA: Protected "8sy9" [edit=sysop:move=sysop]

OCA — Wed, 31 May 2023 04:16:54 GMT

Protected "8sy9" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:16, 31 May 2023

OCA: New page: '''Unreleased structure''' The entry 8sy9 is ON HOLD Authors: Thoden, J.B., Holden, H.M. Description: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epime...

OCA — Wed, 31 May 2023 04:16:53 GMT

New page: '''Unreleased structure''' The entry 8sy9 is ON HOLD Authors: Thoden, J.B., Holden, H.M. Description: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epime...

New page

'''Unreleased structure'''

The entry 8sy9 is ON HOLD

Authors: Thoden, J.B., Holden, H.M.

Description: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid, UDP-N-acetylglucosamoine and UDP at pH 7
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]