8bkd - Revision history

OCA at 11:27, 15 November 2023

OCA — Wed, 15 Nov 2023 11:27:13 GMT

←Older revision		Revision as of 11:27, 15 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8bkd]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[8bkd]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BKD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=URP:N-(AMINOCARBONYL)-BETA-ALANINE'>URP</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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=URP:N-(AMINOCARBONYL)-BETA-ALANINE'>URP</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=8bkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bkd OCA], [https://pdbe.org/8bkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bkd RCSB], [https://www.ebi.ac.uk/pdbsum/8bkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bkd 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=8bkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bkd OCA], [https://pdbe.org/8bkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bkd RCSB], [https://www.ebi.ac.uk/pdbsum/8bkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bkd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:34, 25 January 2023

OCA — Wed, 25 Jan 2023 06:34:46 GMT

←Older revision		Revision as of 06:34, 25 January 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8bkd is ~~ON HOLD until Paper~~ Publication	+	==structure of RutB==
		+	<StructureSection load='8bkd' size='340' side='right'caption='[[8bkd]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8bkd]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BKD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=URP:N-(AMINOCARBONYL)-BETA-ALANINE'>URP</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=8bkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bkd OCA], [https://pdbe.org/8bkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bkd RCSB], [https://www.ebi.ac.uk/pdbsum/8bkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bkd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RUTB_ECOD1 RUTB_ECOD1] Hydrolyzes ureidoacrylate to form aminoacrylate and carbamate. The carbamate hydrolyzes spontaneously, thereby releasing one of the nitrogen atoms of the pyrimidine ring as ammonia and one of its carbon atoms as CO2.[HAMAP-Rule:MF_00830]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 A and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (k(cat)) and/or the Michaelis constant (K(M)). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.

-	~~Authors: Rajendran~~, C.	+	Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli.,Busch MR, Rajendran C, Sterner R Biochemistry. 2023 Jan 4. doi: 10.1021/acs.biochem.2c00640. PMID:36599150<ref>PMID:36599150</ref>

-	~~Description: structure~~ of ~~RutB~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Rajendran, C]]	+	<div class="pdbe-citations 8bkd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli DH1]]
		+	[[Category: Large Structures]]
		+	[[Category: Rajendran C]]

OCA at 05:32, 11 January 2023

OCA — Wed, 11 Jan 2023 05:32:43 GMT

←Older revision		Revision as of 05:32, 11 January 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Rajendran, C.		Authors: Rajendran, C.

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

OCA — Wed, 16 Nov 2022 17:54:59 GMT

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

←Older revision

Revision as of 17:54, 16 November 2022

OCA: New page: '''Unreleased structure''' The entry 8bkd is ON HOLD Authors: Rajendran, C. Description: structure of RutB Category: Unreleased Structures Category: Rajendran, C

OCA — Wed, 16 Nov 2022 17:54:58 GMT

New page: '''Unreleased structure''' The entry 8bkd is ON HOLD Authors: Rajendran, C. Description: structure of RutB Category: Unreleased Structures Category: Rajendran, C

New page

'''Unreleased structure'''

The entry 8bkd is ON HOLD

Authors: Rajendran, C.

Description: structure of RutB
[[Category: Unreleased Structures]]
[[Category: Rajendran, C]]