4e5p - Revision history

OCA at 11:02, 1 March 2024

2024-03-01T11:02:01Z

← Older revision		Revision as of 11:02, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E5P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.9Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [https://pdbe.org/4e5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [https://www.ebi.ac.uk/pdbsum/4e5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e5p 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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [https://pdbe.org/4e5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [https://www.ebi.ac.uk/pdbsum/4e5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e5p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PTXD_PSEST PTXD_PSEST]] Catalyzes phosphite (phosphonate) oxidation.		[https://www.uniprot.org/uniprot/PTXD_PSEST PTXD_PSEST] Catalyzes phosphite (phosphonate) oxidation.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The enzyme phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent conversion of phosphite to phosphate and represents the first biological catalyst that has been shown to conduct the enzymatic oxidation of phosphorus. Despite investigation for more than a decade into both the mechanism of its unusual reaction and its utility in cofactor regeneration, there has been a lack of any structural data for PTDH. Here we present the cocrystal structure of an engineered thermostable variant of PTDH bound to NAD(+) (1.7 A resolution), as well as four other cocrystal structures of thermostable PTDH and its variants with different ligands (all between 1.85 and 2.3 A resolution). These structures provide a molecular framework for understanding prior mutational analysis and point to additional residues, located in the active site, that may contribute to the enzymatic activity of this highly unusual catalyst.

	Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration.,Zou Y, Zhang H, Brunzelle JS, Johannes TW, Woodyer R, Hung JE, Nair N, van der Donk WA, Zhao H, Nair SK Biochemistry. 2012 May 29;51(21):4263-70. Epub 2012 May 17. PMID:22564171<ref>PMID:22564171</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e5p" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:51, 28 September 2022

2022-09-28T06:51:31Z

← Older revision		Revision as of 06:51, 28 September 2022
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	<StructureSection load='4e5p' size='340' side='right'caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4e5p' size='340' side='right'caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E5P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e5n\|4e5n]], [[4e5k\|4e5k]], [[4e5m\|4e5m]]~~</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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [https://pdbe.org/4e5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [https://www.ebi.ac.uk/pdbsum/4e5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e5p 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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [~~http~~://pdbe.org/4e5p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e5p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e5p ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/PTXD_PSEST PTXD_PSEST]] Catalyzes phosphite (phosphonate) oxidation.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Achromobacter sewerinii bergey et al. 1923]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Nair, S K~~]]		[[Category: Pseudomonas stutzeri]]
	[[Category: ~~Zhang, H~~]]		[[Category: Nair SK]]
	[[Category: ~~Zou, Y~~]]		[[Category: Zhang H]]
	[[Category: ~~D-2-hydroxyacid dehydrogenase]]~~		[[Category: Zou Y]]
	~~[[Category: Oxidoreductase~~]]

OCA at 07:57, 27 March 2019

2019-03-27T07:57:58Z

← Older revision		Revision as of 07:57, 27 March 2019
Line 1:		Line 1:

	==Thermostable phosphite dehydrogenase A176R variant in complex with NAD==		==Thermostable phosphite dehydrogenase A176R variant in complex with NAD==
	<StructureSection load='4e5p' size='340' side='right' caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4e5p' size='340' side='right'caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E5P FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Achromobacter sewerinii bergey et al. 1923]]		[[Category: Achromobacter sewerinii bergey et al. 1923]]
			[[Category: Large Structures]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]

OCA at 19:12, 11 August 2016

2016-08-11T19:12:30Z

← Older revision		Revision as of 19:12, 11 August 2016
Line 1:		Line 1:

	==Thermostable phosphite dehydrogenase A176R variant in complex with NAD==		==Thermostable phosphite dehydrogenase A176R variant in complex with NAD==
	<StructureSection load='4e5p' size='340' side='right' caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4e5p' size='340' side='right' caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_stutzeri Pseudomonas stutzeri~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E5P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e5n\|4e5n]], [[4e5k\|4e5k]], [[4e5m\|4e5m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e5n\|4e5n]], [[4e5k\|4e5k]], [[4e5m\|4e5m]]</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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [http://www.ebi.ac.uk/pdbsum/4e5p PDBsum]</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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [http://pdbe.org/4e5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [http://www.ebi.ac.uk/pdbsum/4e5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e5p ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4e5p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Pseudomonas stutzeri~~]]		[[Category: Achromobacter sewerinii bergey et al. 1923]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]

OCA at 14:10, 4 January 2015

2015-01-04T14:10:39Z

← Older revision		Revision as of 14:10, 4 January 2015
Line 1:		Line 1:
	[[~~Image~~:~~4e5p~~.~~png~~\|~~left~~\|~~200px~~]]		==Thermostable phosphite dehydrogenase A176R variant in complex with NAD==
			<StructureSection load='4e5p' size='340' side='right' caption='[[4e5p]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e5p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E5P FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e5n\|4e5n]], [[4e5k\|4e5k]], [[4e5m\|4e5m]]</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=4e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e5p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e5p RCSB], [http://www.ebi.ac.uk/pdbsum/4e5p PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The enzyme phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent conversion of phosphite to phosphate and represents the first biological catalyst that has been shown to conduct the enzymatic oxidation of phosphorus. Despite investigation for more than a decade into both the mechanism of its unusual reaction and its utility in cofactor regeneration, there has been a lack of any structural data for PTDH. Here we present the cocrystal structure of an engineered thermostable variant of PTDH bound to NAD(+) (1.7 A resolution), as well as four other cocrystal structures of thermostable PTDH and its variants with different ligands (all between 1.85 and 2.3 A resolution). These structures provide a molecular framework for understanding prior mutational analysis and point to additional residues, located in the active site, that may contribute to the enzymatic activity of this highly unusual catalyst.

	~~<!--~~		Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration.,Zou Y, Zhang H, Brunzelle JS, Johannes TW, Woodyer R, Hung JE, Nair N, van der Donk WA, Zhao H, Nair SK Biochemistry. 2012 May 29;51(21):4263-70. Epub 2012 May 17. PMID:22564171<ref>PMID:22564171</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_4e5p"~~, ~~creates the "Structure Box" on the page~~.
	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display~~.
	-->
	~~{{STRUCTURE_4e5p\| PDB=4e5p \| SCENE= }}~~

	~~===Thermostable phosphite dehydrogenase A176R variant in complex with NAD===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
	~~<!--~~		<references/>
	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_22564171}}, adds the Publication Abstract to~~ the ~~page~~		__TOC__
	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22564171 is the PubMed ID number~~.		</StructureSection>
	-->
	~~{{ABSTRACT_PUBMED_22564171}}~~

	~~==About this Structure==~~
	~~[[4e5p]] is a 6 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E5P OCA].~~

	==~~Reference~~==
	<~~ref group="xtra">PMID:022564171<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Pseudomonas stutzeri]]		[[Category: Pseudomonas stutzeri]]
	[[Category: Nair, S K.]]		[[Category: Nair, S K]]
	[[Category: Zhang, H.]]		[[Category: Zhang, H]]
	[[Category: Zou, Y.]]		[[Category: Zou, Y]]
	[[Category: D-2-hydroxyacid dehydrogenase]]		[[Category: D-2-hydroxyacid dehydrogenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 05:16, 13 June 2012

2012-06-13T05:16:52Z

← Older revision		Revision as of 05:16, 13 June 2012
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	[[Image:4e5p.~~jpg~~\|left\|200px]]		[[Image:4e5p.png\|left\|200px]]

	<!--		<!--

OCA at 05:52, 30 May 2012

2012-05-30T05:52:54Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4e5p.jpg|left|200px]]
-The entry 4e5p is ON HOLD
+<!--
-Authors: Zou, Y., Zhang, H., Nair, S.K.
+===Thermostable phosphite dehydrogenase A176R variant in complex with NAD===
-Description: Thermostable phosphite dehydrogenase A176R variant in complex with NAD

OCA: Protected "4e5p" [edit=sysop:move=sysop]

2012-03-21T07:18:10Z

Protected "4e5p" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:18, 21 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e5p is ON HOLD Authors: Zou, Y., Zhang, H., Nair, S.K. Description: Thermostable phosphite dehydrogenase A176R variant in complex with NAD

2012-03-21T07:18:09Z

New page: '''Unreleased structure''' The entry 4e5p is ON HOLD Authors: Zou, Y., Zhang, H., Nair, S.K. Description: Thermostable phosphite dehydrogenase A176R variant in complex with NAD

New page

'''Unreleased structure'''

The entry 4e5p is ON HOLD

Authors: Zou, Y., Zhang, H., Nair, S.K.

Description: Thermostable phosphite dehydrogenase A176R variant in complex with NAD