7kb0 - Revision history

OCA at 07:17, 3 April 2024

OCA — Wed, 03 Apr 2024 07:17:23 GMT

←Older revision		Revision as of 07:17, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='7kb0' size='340' side='right'caption='[[7kb0]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='7kb0' size='340' side='right'caption='[[7kb0]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kb0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thema Thema~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KB0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kb0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KB0 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=LLP:(2S)-2-AMINO-6~~-[[~~3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL~~]~~METHYLIDENEAMINO~~]~~HEXANOIC+ACID'>LLP</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]] 1.85Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~TM_0882, Tmari_0884~~ ([~~https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=243274 THEMA~~])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=7kb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kb0 OCA], [https://pdbe.org/7kb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kb0 RCSB], [https://www.ebi.ac.uk/pdbsum/7kb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kb0 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=7kb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kb0 OCA], [https://pdbe.org/7kb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kb0 RCSB], [https://www.ebi.ac.uk/pdbsum/7kb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kb0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/METY_THEMA METY_THEMA]] Catalyzes the production of homocysteine from O-acetylhomoserine (OAH) and hydrogen sulfide (H2S), a step in the methionine biosynthesis pathway. Is not able to form cystathionine from O-acetylhomoserine and L-cysteine.<ref>PMID:28640457</ref>	+	[https://www.uniprot.org/uniprot/METY_THEMA METY_THEMA] Catalyzes the production of homocysteine from O-acetylhomoserine (OAH) and hydrogen sulfide (H2S), a step in the methionine biosynthesis pathway. Is not able to form cystathionine from O-acetylhomoserine and L-cysteine.<ref>PMID:28640457</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Bacterial methionine biosynthesis can either take place by the trans-sulfurylation route or by direct sulfurylation. The enzymes responsible for trans-sulfurylation have been characterized extensively because they occur in model organisms such as Escherichia coli. However, direct sulfurylation is actually the predominant route for methionine biosynthesis across the phylogenetic tree. In this pathway, most bacteria use an O-acetylhomoserine aminocarboxypropyltransferase (MetY) to catalyze the formation of homocysteine from O-acetylhomoserine and bisulfide. Despite the widespread distribution of MetY, this pyridoxal 5'-phosphate (PLP)-dependent enzyme remains comparatively understudied. To address this knowledge gap, we have characterized the MetY from Thermotoga maritima (TmMetY). At its optimal temperature of 70 degrees C, TmMetY has a turnover number (apparent kcat = 900 s(-1)) that is 10- to 700-fold higher than the three other MetY enzymes for which data are available. We also present crystal structures of TmMetY in the internal aldimine form and, fortuitously, with a beta,gamma-unsaturated ketimine reaction intermediate. This intermediate is identical to that found in the catalytic cycle of cystathionine gamma-synthase (MetB), which is a homologous enzyme from the trans-sulfurylation pathway. By comparing the TmMetY and MetB structures, we have identified Arg270 as a critical determinant of specificity. It helps to wall off the active site of TmMetY, disfavoring the binding of the first MetB substrate, O-succinylhomoserine. It also ensures a strict specificity for bisulfide as the second substrate of MetY by occluding the larger MetB substrate, cysteine. Overall, this work illuminates the subtle structural mechanisms by which homologous PLP-dependent enzymes can effect different catalytic - and therefore metabolic - outcomes.	+
-		+
-	Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis.,Brewster JL, Pachl P, McKellar JLO, Selmer M, Squire CJ, Patrick WM J Biol Chem. 2021 May 18:100797. doi: 10.1016/j.jbc.2021.100797. PMID:34019879<ref>PMID:34019879</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7kb0" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thema~~]]	+	[[Category: Thermotoga maritima MSB8]]
-	[[Category: Brewster~~, J L~~]]	+	[[Category: Brewster JL]]
-	[[Category: Pachl, P]]	+	[[Category: Pachl P]]
-	[[Category: Patrick~~, W M~~]]	+	[[Category: Patrick WM]]
-	[[Category: Selmer, M]]	+	[[Category: Selmer M]]
-	[[Category: Squire, C]]	+	[[Category: Squire C]]
-	~~[[Category: Active site]]~~	+
-	~~[[Category: Enzyme kinetic]]~~	+
-	~~[[Category: Methionine biosynthesis]]~~	+
-	~~[[Category: Mety]]~~	+
-	~~[[Category: O-acety-l-homoserine aminocarboxypropyltransferase]]~~	+
-	~~[[Category: Thermotoga maritima]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:49, 28 July 2021

OCA — Wed, 28 Jul 2021 10:49:28 GMT

←Older revision		Revision as of 10:49, 28 July 2021
Line 1:		Line 1:

	==O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima with pyridoxal-5-phosphate (PLP) bound in the internal aldimine state==		==O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima with pyridoxal-5-phosphate (PLP) bound in the internal aldimine state==
-	<StructureSection load='7kb0' size='340' side='right'caption='[[7kb0]]' scene=''>	+	<StructureSection load='7kb0' size='340' side='right'caption='[[7kb0]], [[Resolution\|resolution]] 1.85Å' 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=7KB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KB0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kb0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KB0 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=7kb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kb0 OCA], [https://pdbe.org/7kb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kb0 RCSB], [https://www.ebi.ac.uk/pdbsum/7kb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kb0 ProSAT]</span></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0882, Tmari_0884 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=7kb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kb0 OCA], [https://pdbe.org/7kb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kb0 RCSB], [https://www.ebi.ac.uk/pdbsum/7kb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kb0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/METY_THEMA METY_THEMA]] Catalyzes the production of homocysteine from O-acetylhomoserine (OAH) and hydrogen sulfide (H2S), a step in the methionine biosynthesis pathway. Is not able to form cystathionine from O-acetylhomoserine and L-cysteine.<ref>PMID:28640457</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial methionine biosynthesis can either take place by the trans-sulfurylation route or by direct sulfurylation. The enzymes responsible for trans-sulfurylation have been characterized extensively because they occur in model organisms such as Escherichia coli. However, direct sulfurylation is actually the predominant route for methionine biosynthesis across the phylogenetic tree. In this pathway, most bacteria use an O-acetylhomoserine aminocarboxypropyltransferase (MetY) to catalyze the formation of homocysteine from O-acetylhomoserine and bisulfide. Despite the widespread distribution of MetY, this pyridoxal 5'-phosphate (PLP)-dependent enzyme remains comparatively understudied. To address this knowledge gap, we have characterized the MetY from Thermotoga maritima (TmMetY). At its optimal temperature of 70 degrees C, TmMetY has a turnover number (apparent kcat = 900 s(-1)) that is 10- to 700-fold higher than the three other MetY enzymes for which data are available. We also present crystal structures of TmMetY in the internal aldimine form and, fortuitously, with a beta,gamma-unsaturated ketimine reaction intermediate. This intermediate is identical to that found in the catalytic cycle of cystathionine gamma-synthase (MetB), which is a homologous enzyme from the trans-sulfurylation pathway. By comparing the TmMetY and MetB structures, we have identified Arg270 as a critical determinant of specificity. It helps to wall off the active site of TmMetY, disfavoring the binding of the first MetB substrate, O-succinylhomoserine. It also ensures a strict specificity for bisulfide as the second substrate of MetY by occluding the larger MetB substrate, cysteine. Overall, this work illuminates the subtle structural mechanisms by which homologous PLP-dependent enzymes can effect different catalytic - and therefore metabolic - outcomes.
		+
		+	Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis.,Brewster JL, Pachl P, McKellar JLO, Selmer M, Squire CJ, Patrick WM J Biol Chem. 2021 May 18:100797. doi: 10.1016/j.jbc.2021.100797. PMID:34019879<ref>PMID:34019879</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kb0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brewster JL]]	+	[[Category: Thema]]
-	[[Category: Pachl P]]	+	[[Category: Brewster, J L]]
-	[[Category: Patrick WM]]	+	[[Category: Pachl, P]]
-	[[Category: Selmer M]]	+	[[Category: Patrick, W M]]
-	[[Category: Squire C]]	+	[[Category: Selmer, M]]
		+	[[Category: Squire, C]]
		+	[[Category: Active site]]
		+	[[Category: Enzyme kinetic]]
		+	[[Category: Methionine biosynthesis]]
		+	[[Category: Mety]]
		+	[[Category: O-acety-l-homoserine aminocarboxypropyltransferase]]
		+	[[Category: Thermotoga maritima]]
		+	[[Category: Transferase]]

OCA at 07:32, 25 June 2021

OCA — Fri, 25 Jun 2021 07:32:08 GMT

←Older revision		Revision as of 07:32, 25 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7kb0 is ON HOLD until Paper Publication~~	+	==O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima with pyridoxal-5-phosphate (PLP) bound in the internal aldimine state==
-		+	<StructureSection load='7kb0' size='340' side='right'caption='[[7kb0]]' scene=''>
-	~~Authors: Brewster, J.L., Pachl, P., Squire, C., Selmer, M., Patrick, W.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KB0 FirstGlance]. <br>
-	~~Description:~~ O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima with pyridoxal-5-phosphate (PLP) bound in the internal aldimine state	+	</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=7kb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kb0 OCA], [https://pdbe.org/7kb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kb0 RCSB], [https://www.ebi.ac.uk/pdbsum/7kb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kb0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Patrick, W.M~~]]	+	__TOC__
-	[[Category: ~~Selmer, M~~]]	+	</StructureSection>
-	[[Category: ~~Squire, C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Brewster, J.L~~]]	+	[[Category: Brewster JL]]
-	[[Category: ~~Pachl, P~~]]	+	[[Category: Pachl P]]
		+	[[Category: Patrick WM]]
		+	[[Category: Selmer M]]
		+	[[Category: Squire C]]

OCA at 04:20, 14 October 2020

OCA — Wed, 14 Oct 2020 04:20:28 GMT

←Older revision		Revision as of 04:20, 14 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kb0 is ON HOLD	+	The entry 7kb0 is ON HOLD until Paper Publication

	Authors: Brewster, J.L., Pachl, P., Squire, C., Selmer, M., Patrick, W.M.		Authors: Brewster, J.L., Pachl, P., Squire, C., Selmer, M., Patrick, W.M.

-	Description: ~~Complex of~~ O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima ~~and a key reaction intermediate~~	+	Description: O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima with pyridoxal-5-phosphate (PLP) bound in the internal aldimine state
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Patrick, W.M]]		[[Category: Patrick, W.M]]

OCA: Protected "7kb0" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2020 04:52:33 GMT

Protected "7kb0" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kb0 is ON HOLD Authors: Brewster, J.L., Pachl, P., Squire, C., Selmer, M., Patrick, W.M. Description: Complex of O-acety-L-homoserine aminocarboxy...

OCA — Wed, 07 Oct 2020 04:52:32 GMT

New page: '''Unreleased structure''' The entry 7kb0 is ON HOLD Authors: Brewster, J.L., Pachl, P., Squire, C., Selmer, M., Patrick, W.M. Description: Complex of O-acety-L-homoserine aminocarboxy...

New page

'''Unreleased structure'''

The entry 7kb0 is ON HOLD

Authors: Brewster, J.L., Pachl, P., Squire, C., Selmer, M., Patrick, W.M.

Description: Complex of O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima and a key reaction intermediate
[[Category: Unreleased Structures]]
[[Category: Patrick, W.M]]
[[Category: Selmer, M]]
[[Category: Squire, C]]
[[Category: Brewster, J.L]]
[[Category: Pachl, P]]