5xtg - Revision history

OCA at 08:13, 22 November 2023

OCA — Wed, 22 Nov 2023 08:13:29 GMT

←Older revision		Revision as of 08:13, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5xtg' size='340' side='right'caption='[[5xtg]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='5xtg' size='340' side='right'caption='[[5xtg]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xtg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xtg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._MC1 Pseudomonas sp. MC1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XTG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.318Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5xtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtg OCA], [~~http~~://pdbe.org/5xtg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xtg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xtg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtg ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=5xtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtg OCA], [https://pdbe.org/5xtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xtg RCSB], [https://www.ebi.ac.uk/pdbsum/5xtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G9G7I7_9PSED G9G7I7_9PSED]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kim, H W~~]]	+	[[Category: Pseudomonas sp. MC1]]
-	[[Category: ~~Park, A K]]~~	+	[[Category: Kim H-W]]
-	~~[[Category: Cis~~-~~dihydrodiol naphthalene dehydrogenase~~]]	+	[[Category: Park AK]]
-	[[Category: ~~Oxidoreductase]]~~	+
-	~~[[Category: Tetramer~~]]	+

OCA at 06:58, 14 October 2020

OCA — Wed, 14 Oct 2020 06:58:40 GMT

←Older revision		Revision as of 06:58, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1 in the presence of NAD+ and 2,3-dihydroxybiphenyl==		==Crystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1 in the presence of NAD+ and 2,3-dihydroxybiphenyl==
-	<StructureSection load='5xtg' size='340' side='right' caption='[[5xtg]], [[Resolution\|resolution]] 2.32Å' scene=''>	+	<StructureSection load='5xtg' size='340' side='right'caption='[[5xtg]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xtg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xtg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XTG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=5xtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtg OCA], [http://pdbe.org/5xtg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xtg RCSB], [http://www.ebi.ac.uk/pdbsum/5xtg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtg ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtg OCA], [http://pdbe.org/5xtg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xtg RCSB], [http://www.ebi.ac.uk/pdbsum/5xtg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kim, H W]]		[[Category: Kim, H W]]
	[[Category: Park, A K]]		[[Category: Park, A K]]

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

OCA — Wed, 09 Aug 2017 09:02:02 GMT

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

←Older revision

Revision as of 09:02, 9 August 2017

OCA: New page: ==Crystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1 in the presence of NAD+ and 2,3-dihydroxybiphenyl== == Structural highlights ==
<table><tr><td colspan='2'>[[5xtg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XTG FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=5xtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtg OCA], [http://pdbe.org/5xtg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xtg RCSB], [http://www.ebi.ac.uk/pdbsum/5xtg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtg ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The bacterial strain Pseudomonas sp. MC1 harbors an 81-kb metabolic plasmid, which encodes enzymes involved in the conversion of naphthalene to salicylate. Of these, the enzyme NahB (cis-dihydrodiol naphthalene dehydrogenase), which catalyzes the second reaction of this pathway, binds to various substrates such as cis-1,2-dihydro-1,2-dihydroxy-naphthalene (1,2-DDN), cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDB), and 3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl (3,4-DD-2,2',5-5-TCB). However, the mechanism underlying its broad substrate specificity is unclear owing to the lack of structural information. Here, we determined the first crystal structures of NahB in the absence and presence of NAD+ and 2,3-dihydroxybiphenyl (2,3-DB). Structure analysis suggests that the flexible substrate-binding loop allows NahB to accommodate diverse substrates. Furthermore, we defined the initial steps of substrate recognition and identified the early substrate-binding site in the substrate recognition process through the complex structure with ligands.

Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate.,Park AK, Kim H, Kim IS, Roh SJ, Shin SC, Lee JH, Park H, Kim HW Biochem Biophys Res Commun. 2017 Jul 17. pii: S0006-291X(17)31439-0. doi:, 10.1016/j.bbrc.2017.07.089. PMID:28728845<ref>PMID:28728845</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xtg" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Kim, H W]]
[[Category: Park, A K]]
[[Category: Cis-dihydrodiol naphthalene dehydrogenase]]
[[Category: Oxidoreductase]]
[[Category: Tetramer]]