6npa - Revision history

OCA at 06:57, 11 October 2023

OCA — Wed, 11 Oct 2023 06:57:23 GMT

←Older revision		Revision as of 06:57, 11 October 2023
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	<StructureSection load='6npa' size='340' side='right'caption='[[6npa]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6npa' size='340' side='right'caption='[[6npa]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6npa]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ccug_55859 Ccug 55859~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6npa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Leisingera_caerulea Leisingera caerulea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NPA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=KVP:(2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium'>KVP</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]] 1.73Å</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=6npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npa OCA], [~~http~~://pdbe.org/6npa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6npa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6npa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6npa ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=KVP:(2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium'>KVP</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=6npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npa OCA], [https://pdbe.org/6npa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6npa RCSB], [https://www.ebi.ac.uk/pdbsum/6npa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6npa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A4V8H040_9RHOB A0A4V8H040_9RHOB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ccug 55859]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Boal, A K~~]]	+	[[Category: Leisingera caerulea]]
-	[[Category: ~~Mitchell, A J~~]]	+	[[Category: Boal AK]]
-	[[Category: ~~Rajakovich, L J~~]]	+	[[Category: Mitchell AJ]]
-	[[Category: ~~Enzyme]]~~	+	[[Category: Rajakovich LJ]]
-	~~[[Category: Gene annotation]]~~	+
-	~~[[Category: Hd-domain]]~~	+
-	~~[[Category: Iron oxygenase]]~~	+
-	~~[[Category: Organophosphonate]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:58, 10 April 2019

OCA — Wed, 10 Apr 2019 07:58:32 GMT

←Older revision		Revision as of 07:58, 10 April 2019
Line 1:		Line 1:

	==X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase, with (R)-1-hydroxy-2-trimethylaminoethylphosphonate==		==X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase, with (R)-1-hydroxy-2-trimethylaminoethylphosphonate==
-	<StructureSection load='6npa' size='340' side='right' caption='[[6npa]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='6npa' size='340' side='right'caption='[[6npa]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6npa]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6npa]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ccug_55859 Ccug 55859]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NPA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=KVP:(2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium'>KVP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=KVP:(2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium'>KVP</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=6npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npa OCA], [http://pdbe.org/6npa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6npa RCSB], [http://www.ebi.ac.uk/pdbsum/6npa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6npa 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=6npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npa OCA], [http://pdbe.org/6npa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6npa RCSB], [http://www.ebi.ac.uk/pdbsum/6npa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6npa ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ccug 55859]]
		+	[[Category: Large Structures]]
	[[Category: Boal, A K]]		[[Category: Boal, A K]]
	[[Category: Mitchell, A J]]		[[Category: Mitchell, A J]]

OCA at 07:35, 6 March 2019

OCA — Wed, 06 Mar 2019 07:35:36 GMT

←Older revision		Revision as of 07:35, 6 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6npa ~~is ON HOLD~~ ~~until Paper~~ Publication	+	==X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase, with (R)-1-hydroxy-2-trimethylaminoethylphosphonate==
		+	<StructureSection load='6npa' size='340' side='right' caption='[[6npa]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6npa]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NPA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=KVP:(2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium'>KVP</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=6npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npa OCA], [http://pdbe.org/6npa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6npa RCSB], [http://www.ebi.ac.uk/pdbsum/6npa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6npa ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The assignment of biochemical functions to hypothetical proteins is challenged by functional diversification within many protein structural superfamilies. This diversification, which is particularly common for metalloenzymes, renders functional annotations that are founded solely on sequence and domain similarities unreliable and often erroneous. Definitive biochemical characterization to delineate functional sub-groups within these superfamilies will aid in improving bioinformatic approaches for functional annotation. We describe here the structural and functional characterization of two non-heme-iron oxygenases, TmpA and TmpB, which are encoded by a genomically clustered pair of genes found in more than 350 species of bacteria. TmpA and TmpB are functional homologues of a pair of enzymes (PhnY and PhnZ) that degrade 2-aminoethylphosphonate but instead act on its naturally occurring, quaternary ammonium analogue, 2-(trimethylammonio)ethylphosphonate (TMAEP). TmpA, an iron(II)- and 2-(oxo)glutarate-dependent oxygenase misannotated as a gamma-butyrobetaine (gammabb) hydroxylase, shows no activity toward gammabb but efficiently hydroxylates TMAEP. The product, (R)-1-hydroxy-2-(trimethylammonio)ethylphosphonate [(R)-OH-TMAEP], then serves as the substrate for the second enzyme, TmpB. By contrast to its purported phosphohydrolytic activity, TmpB is an HD-domain oxygenase that uses a mixed-valent diiron cofactor to enact oxidative cleavage of the C-P bond of its substrate, yielding glycine betaine and phosphate. The high specificities of TmpA and TmpB for their N-trimethylated substrates suggests that they have evolved specifically to degrade TMAEP, which was not previously known to be subject to microbial catabolism. This study thus adds to the growing list of known pathways through which microbes break down organophosphonates to harvest phosphorus, carbon, and nitrogen in nutrient-limited niches.

-	~~Authors~~:	+	A new microbial pathway for organophosphonate degradation catalyzed by two previously misannotated non-heme-iron oxygenases.,Rajakovich L, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM Jr Biochemistry. 2019 Feb 21. doi: 10.1021/acs.biochem.9b00044. PMID:30789718<ref>PMID:30789718</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6npa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boal, A K]]
		+	[[Category: Mitchell, A J]]
		+	[[Category: Rajakovich, L J]]
		+	[[Category: Enzyme]]
		+	[[Category: Gene annotation]]
		+	[[Category: Hd-domain]]
		+	[[Category: Iron oxygenase]]
		+	[[Category: Organophosphonate]]
		+	[[Category: Oxidoreductase]]

OCA at 07:36, 13 February 2019

OCA — Wed, 13 Feb 2019 07:36:24 GMT

←Older revision		Revision as of 07:36, 13 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6npa is ON HOLD	+	The entry 6npa is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6npa" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2019 06:42:40 GMT

Protected "6npa" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:42, 30 January 2019

OCA: New page: '''Unreleased structure''' The entry 6npa is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Jan 2019 06:42:39 GMT

New page: '''Unreleased structure''' The entry 6npa is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6npa is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]