7bcn - Revision history

OCA at 12:25, 1 February 2024

OCA — Thu, 01 Feb 2024 12:25:48 GMT

←Older revision		Revision as of 12:25, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7bcn' size='340' side='right'caption='[[7bcn]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='7bcn' size='340' side='right'caption='[[7bcn]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7bcn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Advmd Advmd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bcn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Advenella_mimigardefordensis_DPN7 Advenella mimigardefordensis DPN7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BCN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=TK8:D~~-~~xylonic+acid'>TK8</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[7bbr\|7bbr]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TK8:D-xylonic+acid'>TK8</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIM_c39430 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1247726 ADVMD])~~</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=7bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bcn OCA], [https://pdbe.org/7bcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bcn RCSB], [https://www.ebi.ac.uk/pdbsum/7bcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bcn 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=7bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bcn OCA], [https://pdbe.org/7bcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bcn RCSB], [https://www.ebi.ac.uk/pdbsum/7bcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bcn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/R4JTF7_ADVMD R4JTF7_ADVMD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Advmd~~]]	+	[[Category: Advenella mimigardefordensis DPN7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hoeppner, A]]	+	[[Category: Hoeppner A]]
-	[[Category: Kobus, S]]	+	[[Category: Kobus S]]
-	[[Category: Meinert, C]]	+	[[Category: Meinert C]]
-	[[Category: Schaefer, L]]	+	[[Category: Schaefer L]]
-	[[Category: Smits~~, S H~~]]	+	[[Category: Smits SH]]
-	[[Category: Steinbuechel, A]]	+	[[Category: Steinbuechel A]]
-	~~[[Category: Transport binding protein sugar binding]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 06:29, 25 August 2021

OCA — Wed, 25 Aug 2021 06:29:30 GMT

←Older revision		Revision as of 06:29, 25 August 2021
Line 1:		Line 1:

	==Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid==		==Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid==
-	<StructureSection load='7bcn' size='340' side='right'caption='[[7bcn]]' scene=''>	+	<StructureSection load='7bcn' size='340' side='right'caption='[[7bcn]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bcn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Advmd Advmd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BCN FirstGlance]. <br>
-	</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=7bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bcn OCA], [https://pdbe.org/7bcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bcn RCSB], [https://www.ebi.ac.uk/pdbsum/7bcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bcn ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TK8:D-xylonic+acid'>TK8</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7bbr\|7bbr]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIM_c39430 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1247726 ADVMD])</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=7bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bcn OCA], [https://pdbe.org/7bcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bcn RCSB], [https://www.ebi.ac.uk/pdbsum/7bcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bcn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Recently, CxaP, a sugar acid substrate binding protein (SBP) from Advenella mimigardefordensis strain DPN7(T) , was identified as part of a novel sugar uptake strategy. In the present study, the protein was successfully crystallized. Although several SBP structures of tripartite ATP-independent periplasmic transporters have already been solved, this is the first structure of an SBP accepting multiple sugar acid ligands. Protein crystals were obtained with bound d-xylonic acid, d-fuconic acid d-galactonic and d-gluconic acid, respectively. The protein shows the typical structure of an SBP of a tripartite ATP-independent periplasmic transporter consisting of two domains linked by a hinge and spanned by a long alpha-helix. By analysis of the structure, the substrate binding site of the protein was identified. The carboxylic group of the sugar acids interacts with Arg175, whereas the coordination of the hydroxylic groups at positions C2 and C3 is most probably realized by Arg154 and Asn151. Furthermore, it was observed that 2-keto-3-deoxy-d-gluconic acid is bound in protein crystals that were crystallized without the addition of any ligand, indicating that this molecule is prebound to the protein and is displaced by the other ligands if they are available. DATABASE: Structural data of CxaP complexes are available in the worldwide Protein Data Bank (https://www.rcsb.org) under the accession codes 7BBR (2-keto-3-deoxy-d-gluconic acid), 7BCR (d-galactonic acid), 7BCN (d-xylonic acid), 7BCO (d-fuconic acid) and 7BCP (d-gluconic acid).
		+
		+	Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7(T).,Schafer L, Meinert-Berning C, Kobus S, Hoppner A, Smits SHJ, Steinbuchel A FEBS J. 2021 Feb 25. doi: 10.1111/febs.15789. PMID:33630388<ref>PMID:33630388</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bcn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Advmd]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hoeppner A]]	+	[[Category: Hoeppner, A]]
-	[[Category: Kobus S]]	+	[[Category: Kobus, S]]
-	[[Category: Meinert C]]	+	[[Category: Meinert, C]]
-	[[Category: Schaefer L]]	+	[[Category: Schaefer, L]]
-	[[Category: Smits SH]]	+	[[Category: Smits, S H]]
-	[[Category: Steinbuechel A]]	+	[[Category: Steinbuechel, A]]
		+	[[Category: Transport binding protein sugar binding]]
		+	[[Category: Transport protein]]

OCA at 06:45, 14 April 2021

OCA — Wed, 14 Apr 2021 06:45:29 GMT

←Older revision		Revision as of 06:45, 14 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7bcn is ON HOLD~~	+	==Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid==
-		+	<StructureSection load='7bcn' size='340' side='right'caption='[[7bcn]]' scene=''>
-	~~Authors: Schaefer, L., Meinert, C., Kobus, S., Hoeppner, A., Smits, S.H., Steinbuechel, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BCN FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid	+	</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=7bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bcn OCA], [https://pdbe.org/7bcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bcn RCSB], [https://www.ebi.ac.uk/pdbsum/7bcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bcn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Hoeppner, A]]	+	__TOC__
-	[[Category: ~~Smits,~~ S.H]]	+	</StructureSection>
-	[[Category: ~~Kobus, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Steinbuechel, A~~]]	+	[[Category: Hoeppner A]]
-	[[Category: ~~Schaefer, L~~]]	+	[[Category: Kobus S]]
-	[[Category: ~~Meinert, C~~]]	+	[[Category: Meinert C]]
		+	[[Category: Schaefer L]]
		+	[[Category: Smits SH]]
		+	[[Category: Steinbuechel A]]

OCA at 04:26, 7 April 2021

OCA — Wed, 07 Apr 2021 04:26:19 GMT

←Older revision		Revision as of 04:26, 7 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7bcn is ON HOLD ~~until sometime in the future~~	+	The entry 7bcn is ON HOLD

	Authors: Schaefer, L., Meinert, C., Kobus, S., Hoeppner, A., Smits, S.H., Steinbuechel, A.		Authors: Schaefer, L., Meinert, C., Kobus, S., Hoeppner, A., Smits, S.H., Steinbuechel, A.

OCA: Protected "7bcn" [edit=sysop:move=sysop]

OCA — Wed, 30 Dec 2020 05:16:24 GMT

Protected "7bcn" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:16, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7bcn is ON HOLD until sometime in the future Authors: Schaefer, L., Meinert, C., Kobus, S., Hoeppner, A., Smits, S.H., Steinbuechel, A. Description...

OCA — Wed, 30 Dec 2020 05:16:23 GMT

New page: '''Unreleased structure''' The entry 7bcn is ON HOLD until sometime in the future Authors: Schaefer, L., Meinert, C., Kobus, S., Hoeppner, A., Smits, S.H., Steinbuechel, A. Description...

New page

'''Unreleased structure'''

The entry 7bcn is ON HOLD until sometime in the future

Authors: Schaefer, L., Meinert, C., Kobus, S., Hoeppner, A., Smits, S.H., Steinbuechel, A.

Description: Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid
[[Category: Unreleased Structures]]
[[Category: Hoeppner, A]]
[[Category: Smits, S.H]]
[[Category: Kobus, S]]
[[Category: Steinbuechel, A]]
[[Category: Schaefer, L]]
[[Category: Meinert, C]]