5epd - Revision history

OCA at 08:13, 12 July 2023

OCA — Wed, 12 Jul 2023 08:13:46 GMT

←Older revision		Revision as of 08:13, 12 July 2023
Line 1:		Line 1:

	==Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)==		==Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)==
-	<StructureSection load='5epd' size='340' side='right' caption='[[5epd]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5epd' size='340' side='right'caption='[[5epd]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5epd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5epd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EPD FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[4jic\|4jic]]</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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">xdpB ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])~~</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=5epd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epd OCA], [https://pdbe.org/5epd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5epd RCSB], [https://www.ebi.ac.uk/pdbsum/5epd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5epd 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=5epd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epd OCA], [~~http~~://pdbe.org/5epd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5epd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5epd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5epd ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0A0VDJ9_RHIRD A0A0A0VDJ9_RHIRD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cerny, J~~]]	+	[[Category: Agrobacterium tumefaciens]]
-	[[Category: ~~Kolenko, P~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kyslikova, E~~]]	+	[[Category: Cerny J]]
-	[[Category: ~~Palyzova, A~~]]	+	[[Category: Kolenko P]]
-	[[Category: ~~Schneider, B~~]]	+	[[Category: Kyslikova E]]
-	[[Category: ~~Zahradnik, J~~]]	+	[[Category: Palyzova A]]
-	[[Category: ~~Zuskova, I~~]]	+	[[Category: Schneider B]]
-	[[Category: ~~Old Yellow Enzyme~~]]	+	[[Category: Zahradnik J]]
-	[[Category: ~~Oxidorecctase~~]]	+	[[Category: Zuskova I]]

OCA at 15:48, 27 February 2019

OCA — Wed, 27 Feb 2019 15:48:07 GMT

←Older revision		Revision as of 15:48, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='5epd' size='340' side='right' caption='[[5epd]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5epd' size='340' side='right' caption='[[5epd]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5epd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5epd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EPD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xdpB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=5epd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epd OCA], [http://pdbe.org/5epd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5epd RCSB], [http://www.ebi.ac.uk/pdbsum/5epd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5epd 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=5epd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epd OCA], [http://pdbe.org/5epd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5epd RCSB], [http://www.ebi.ac.uk/pdbsum/5epd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5epd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Old Yellow Enzymes (OYEs) are NAD(P)H dehydrogenases of not fully resolved physiological roles that are widespread among bacteria, plants, and fungi and have a great potential for biotechnological applications. We determined the apo form crystal structure of a member of the OYE class, glycerol trinitrate reductase XdpB, from Agrobacterium bohemicum R89-1 at 2.1 A resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal beta-hairpin lid, but surprisingly, the structure did not contain its cofactor FMN. Its putative binding site was occupied by a pentapeptide TTSDN from the C-terminus of a symmetry related molecule. Biochemical experiments confirmed a specific concentration-dependent oligomerization and a low FMN content. The blocking of the FMN binding site can exist in vivo and regulates enzyme activity. Our bioinformatic analysis indicated that a similar self-inhibition could be expected in more OYEs which we designated as subgroup OYE C1. This subgroup is widespread among G-bacteria and can be recognized by the conserved sequence GxxDYP in proximity of the C termini. In proteobacteria, the C1 subgroup OYEs are typically coded in one operon with short-chain dehydrogenase. This operon is controlled by the tetR-like transcriptional regulator. OYEs coded in these operons are unlikely to be involved in the oxidative stress response as the other known members of the OYE family because no upregulation of XdpB was observed after exposing A. bohemicum R89-1 to oxidative stress.
		+
		+	The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.,Zahradnik J, Kolenko P, Palyzova A, Cerny J, Kolarova L, Kyslikova E, Maresova H, Grulich M, Nunvar J, Sulc M, Kyslik P, Schneider B PLoS One. 2018 Apr 9;13(4):e0195299. doi: 10.1371/journal.pone.0195299., eCollection 2018. PMID:29630677<ref>PMID:29630677</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5epd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:48, 10 December 2016

OCA — Sat, 10 Dec 2016 10:48:22 GMT

←Older revision		Revision as of 10:48, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5epd is ON HOLD until Paper Publication~~	+	==Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)==
-		+	<StructureSection load='5epd' size='340' side='right' caption='[[5epd]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors: Kolenko, P., Zahradnik, J., Zuskova, I., Cerny, J., Palyzova, A., Kyslikova, E., Schneider, B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5epd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EPD FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jic\|4jic]]</td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	<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=5epd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epd OCA], [http://pdbe.org/5epd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5epd RCSB], [http://www.ebi.ac.uk/pdbsum/5epd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5epd ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Zahradnik, J~~]]	+	</table>
-	[[~~Category~~: ~~Zuskova, I~~]]	+	__TOC__
-	[[~~Category~~: ~~Schneider~~, B]]	+	</StructureSection>
	[[Category: Cerny, J]]		[[Category: Cerny, J]]
		+	[[Category: Kolenko, P]]
	[[Category: Kyslikova, E]]		[[Category: Kyslikova, E]]
	[[Category: Palyzova, A]]		[[Category: Palyzova, A]]
-	[[Category: ~~Kolenko~~, P]]	+	[[Category: Schneider, B]]
		+	[[Category: Zahradnik, J]]
		+	[[Category: Zuskova, I]]
		+	[[Category: Old Yellow Enzyme]]
		+	[[Category: Oxidorecctase]]

OCA at 10:49, 19 October 2016

OCA — Wed, 19 Oct 2016 10:49:43 GMT

←Older revision		Revision as of 10:49, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kolenko, P., Zahradnik, J., Zuskova, I., Cerny, J., Palyzova, A., Kyslikova, E., Schneider, B.		Authors: Kolenko, P., Zahradnik, J., Zuskova, I., Cerny, J., Palyzova, A., Kyslikova, E., Schneider, B.

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

OCA — Tue, 01 Dec 2015 03:10:39 GMT

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

←Older revision

Revision as of 03:10, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5epd is ON HOLD Authors: Kolenko, P., Zahradnik, J., Zuskova, I., Cerny, J., Palyzova, A., Kyslikova, E., Schneider, B. Description: Crystal struct...

OCA — Tue, 01 Dec 2015 03:10:38 GMT

New page: '''Unreleased structure''' The entry 5epd is ON HOLD Authors: Kolenko, P., Zahradnik, J., Zuskova, I., Cerny, J., Palyzova, A., Kyslikova, E., Schneider, B. Description: Crystal struct...

New page

'''Unreleased structure'''

The entry 5epd is ON HOLD

Authors: Kolenko, P., Zahradnik, J., Zuskova, I., Cerny, J., Palyzova, A., Kyslikova, E., Schneider, B.

Description: Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)
[[Category: Unreleased Structures]]
[[Category: Zahradnik, J]]
[[Category: Zuskova, I]]
[[Category: Schneider, B]]
[[Category: Cerny, J]]
[[Category: Kyslikova, E]]
[[Category: Palyzova, A]]
[[Category: Kolenko, P]]