5x3d - Revision history

OCA at 10:17, 27 March 2024

OCA — Wed, 27 Mar 2024 10:17:02 GMT

←Older revision		Revision as of 10:17, 27 March 2024
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	<StructureSection load='5x3d' size='340' side='right'caption='[[5x3d]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='5x3d' size='340' side='right'caption='[[5x3d]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X3D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_wedmorensis Streptomyces wedmorensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X3D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</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]] 1.93Å</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=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [~~http~~://pdbe.org/5x3d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</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=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [https://pdbe.org/5x3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [https://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/FOM1_STRWE FOM1_STRWE] Bifunctional enzyme that catalyzes two steps during fosfomycin biosynthesis (PubMed:28727444). It catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy), the first step of the pathway. It also catalyzes the cytidylylation of the 2-hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-2-hydroxyethylphosphonate (HEP-CMP), the fourth step of the pathway (PubMed:28727444).<ref>PMID:28727444</ref>
-	~~Fosfomycin is a wide-spectrum phosphonate antibiotic~~ that ~~is used clinically to treat cystitis, tympanitis, etc~~. ~~Its biosynthesis starts with~~ the ~~formation~~ of ~~a carbon-phosphorus bond catalyzed by the~~ phosphoenolpyruvate ~~phosphomutase Fom1. We identified an additional cytidylyltransferase~~ (~~CyTase~~) ~~domain at the Fom1 N-terminus in addition~~ to the ~~phosphoenolpyruvate phosphomutase domain at~~ the ~~Fom1 C-terminus~~. ~~Here, we demonstrate that Fom1 is bifunctional and that the Fom1 CyTase domain~~ catalyzes the cytidylylation of the 2-hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-HEP. On the basis of this new function of Fom1, we propose a revised fosfomycin biosynthetic pathway that involves the transient CMP-conjugated intermediate. The identification of a biosynthetic mechanism via such transient cytidylylation of a biosynthetic intermediate fundamentally advances the understanding of phosphonate biosynthesis in nature. The crystal structure of the cytidylyl-HEP-~~bound CyTase domain provides a basis for~~ the ~~substrate specificity and reveals unique catalytic elements not found in other members~~ of the ~~CyTase family.~~	+
-		+
-	Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme.,Cho SH, Kim SY, Tomita T, Shiraishi T, Park JS, Sato S, Kudo F, Eguchi T, Funa N, Nishiyama M, Kuzuyama T ACS Chem Biol. 2017 Aug 18;12(8)~~:2209-2215~~. ~~doi: 10.1021/acschembio.7b00419. Epub, 2017 Jul 20. PMID:28727444~~<ref>PMID:28727444</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5x3d" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cho, S H~~]]	+	[[Category: Streptomyces wedmorensis]]
-	[[Category: ~~Kuzuyama, T~~]]	+	[[Category: Cho SH]]
-	[[Category: ~~Nishiyama, M]]~~	+	[[Category: Kuzuyama T]]
-	~~[[Category: Tomita,~~ T]]	+	[[Category: Nishiyama M]]
-	[[Category: ~~Cytidylyltransferase~~]]	+	[[Category: Tomita T]]
-	[[Category: ~~Fosfomycin biosynthesis]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:23, 7 October 2020

OCA — Wed, 07 Oct 2020 07:23:54 GMT

←Older revision		Revision as of 07:23, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis==		==Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis==
-	<StructureSection load='5x3d' size='340' side='right' caption='[[5x3d]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='5x3d' size='340' side='right'caption='[[5x3d]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X3D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X3D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</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=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [http://pdbe.org/5x3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [http://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d 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=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [http://pdbe.org/5x3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [http://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cho, S H]]		[[Category: Cho, S H]]
	[[Category: Kuzuyama, T]]		[[Category: Kuzuyama, T]]

OCA at 10:42, 13 September 2017

OCA — Wed, 13 Sep 2017 10:42:02 GMT

←Older revision		Revision as of 10:42, 13 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x3d is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis==
		+	<StructureSection load='5x3d' size='340' side='right' caption='[[5x3d]], [[Resolution\|resolution]] 1.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X3D FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</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=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [http://pdbe.org/5x3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [http://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fosfomycin is a wide-spectrum phosphonate antibiotic that is used clinically to treat cystitis, tympanitis, etc. Its biosynthesis starts with the formation of a carbon-phosphorus bond catalyzed by the phosphoenolpyruvate phosphomutase Fom1. We identified an additional cytidylyltransferase (CyTase) domain at the Fom1 N-terminus in addition to the phosphoenolpyruvate phosphomutase domain at the Fom1 C-terminus. Here, we demonstrate that Fom1 is bifunctional and that the Fom1 CyTase domain catalyzes the cytidylylation of the 2-hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-HEP. On the basis of this new function of Fom1, we propose a revised fosfomycin biosynthetic pathway that involves the transient CMP-conjugated intermediate. The identification of a biosynthetic mechanism via such transient cytidylylation of a biosynthetic intermediate fundamentally advances the understanding of phosphonate biosynthesis in nature. The crystal structure of the cytidylyl-HEP-bound CyTase domain provides a basis for the substrate specificity and reveals unique catalytic elements not found in other members of the CyTase family.

-	~~Authors:~~ Tomita, T., ~~Cho~~, S~~.H.~~, ~~Kuzuyama~~, T., ~~Nishiyama~~, M.	+	Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme.,Cho SH, Kim SY, Tomita T, Shiraishi T, Park JS, Sato S, Kudo F, Eguchi T, Funa N, Nishiyama M, Kuzuyama T ACS Chem Biol. 2017 Aug 18;12(8):2209-2215. doi: 10.1021/acschembio.7b00419. Epub, 2017 Jul 20. PMID:28727444<ref>PMID:28727444</ref>

-	~~Description: Crystal structure~~ of ~~HEP~~-~~CMP~~-~~bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Tomita, T]]~~	+	<div class="pdbe-citations 5x3d" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Nishiyama~~, M]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cho, S H]]
	[[Category: Kuzuyama, T]]		[[Category: Kuzuyama, T]]
-	[[Category: ~~Cho~~, ~~S.H~~]]	+	[[Category: Nishiyama, M]]
		+	[[Category: Tomita, T]]
		+	[[Category: Cytidylyltransferase]]
		+	[[Category: Fosfomycin biosynthesis]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Transferase]]

OCA: Protected "5x3d" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:41:42 GMT

Protected "5x3d" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:41, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x3d is ON HOLD until Paper Publication Authors: Tomita, T., Cho, S.H., Kuzuyama, T., Nishiyama, M. Description: Crystal structure of HEP-CMP-bound...

OCA — Thu, 09 Mar 2017 15:41:41 GMT

New page: '''Unreleased structure''' The entry 5x3d is ON HOLD until Paper Publication Authors: Tomita, T., Cho, S.H., Kuzuyama, T., Nishiyama, M. Description: Crystal structure of HEP-CMP-bound...

New page

'''Unreleased structure'''

The entry 5x3d is ON HOLD until Paper Publication

Authors: Tomita, T., Cho, S.H., Kuzuyama, T., Nishiyama, M.

Description: Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis
[[Category: Unreleased Structures]]
[[Category: Tomita, T]]
[[Category: Nishiyama, M]]
[[Category: Kuzuyama, T]]
[[Category: Cho, S.H]]