6dyv - Revision history

OCA at 06:16, 11 October 2023

OCA — Wed, 11 Oct 2023 06:16:25 GMT

←Older revision		Revision as of 06:16, 11 October 2023
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	<StructureSection load='6dyv' size='340' side='right'caption='[[6dyv]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='6dyv' size='340' side='right'caption='[[6dyv]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dyv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43504 Atcc 43504~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DYV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dyv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OS3:(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol'>OS3</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]] 1.62Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BW246_00770, BZL55_04980, CEP79_03920 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OS3:(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol'>OS3</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylhomocysteine_nucleosidase Adenosylhomocysteine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.9 3.2.2.9] </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=6dyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dyv OCA], [https://pdbe.org/6dyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dyv RCSB], [https://www.ebi.ac.uk/pdbsum/6dyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dyv 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=6dyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dyv OCA], [~~http~~://pdbe.org/6dyv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dyv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dyv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dyv ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A1W0VQJ9_HELPX A0A1W0VQJ9_HELPX]~~] Catalyzes the ~~irreversible cleavage~~ of the glycosidic bond in ~~both~~ 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH~~/AdoHcy~~) to adenine and the ~~corresponding thioribose~~, 5'-~~methylthioribose~~ and S-~~ribosylhomocysteine, respectively~~.~~[SAAS~~:~~SAAS00131143]~~	+	[https://www.uniprot.org/uniprot/MQMTN_HELPJ MQMTN_HELPJ] Catalyzes the direct conversion of aminodeoxyfutalosine (AFL) into dehypoxanthine futalosine (DHFL) and adenine via the hydrolysis of the N-glycosidic bond; this reaction seems to represent an essential step in the menaquinone biosynthesis pathway in Helicobacter species. Also catalyzes the hydrolysis of 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Can also probably use S-adenosylhomocysteine (SAH) as substrate, leading to adenine and S-ribosylhomocysteine. These other activities highlight the tremendous versatility of the enzyme, which also plays key roles in S-adenosylmethionine recycling and in the biosynthesis of the quorum-sensing molecule autoinducer-2.<ref>PMID:20954236</ref> <ref>PMID:22891633</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Adenosylhomocysteine nucleosidase]]~~	+	[[Category: Helicobacter pylori]]
-	~~[[Category: Atcc 43504~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Almo SC]]
-	[[Category: Bonanno~~, J B~~]]	+	[[Category: Bonanno JB]]
-	[[Category: Ducati~~, R G~~]]	+	[[Category: Ducati RG]]
-	[[Category: Harijan~~, R K~~]]	+	[[Category: Harijan RK]]
-	[[Category: Schramm~~, V L]]~~	+	[[Category: Schramm VL]]
-	~~[[Category: Duodenal ulcer]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Mtan enzyme]]~~	+
-	~~[[Category: Stomach cancer~~]]	+

OCA at 07:47, 10 April 2019

OCA — Wed, 10 Apr 2019 07:47:01 GMT

←Older revision		Revision as of 07:47, 10 April 2019
Line 3:		Line 3:
	<StructureSection load='6dyv' size='340' side='right'caption='[[6dyv]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='6dyv' size='340' side='right'caption='[[6dyv]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dyv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DYV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OS3:(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol'>OS3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OS3:(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol'>OS3</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BW246_00770, BZL55_04980, CEP79_03920 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylhomocysteine_nucleosidase Adenosylhomocysteine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.9 3.2.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylhomocysteine_nucleosidase Adenosylhomocysteine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.9 3.2.2.9] </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=6dyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dyv OCA], [http://pdbe.org/6dyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dyv RCSB], [http://www.ebi.ac.uk/pdbsum/6dyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dyv 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=6dyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dyv OCA], [http://pdbe.org/6dyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dyv RCSB], [http://www.ebi.ac.uk/pdbsum/6dyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dyv ProSAT]</span></td></tr>
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Adenosylhomocysteine nucleosidase]]		[[Category: Adenosylhomocysteine nucleosidase]]
		+	[[Category: Atcc 43504]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 07:49, 20 March 2019

OCA — Wed, 20 Mar 2019 07:49:11 GMT

←Older revision		Revision as of 07:49, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dyv is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol==
		+	<StructureSection load='6dyv' size='340' side='right'caption='[[6dyv]], [[Resolution\|resolution]] 1.62Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dyv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DYV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OS3:(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol'>OS3</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylhomocysteine_nucleosidase Adenosylhomocysteine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.9 3.2.2.9] </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=6dyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dyv OCA], [http://pdbe.org/6dyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dyv RCSB], [http://www.ebi.ac.uk/pdbsum/6dyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dyv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A1W0VQJ9_HELPX A0A1W0VQJ9_HELPX]] Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively.[SAAS:SAAS00131143]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) catalyzes the hydrolysis of adenine from S-methyl-5'-thioadenosine (MTA) and S-adenosyl L-homocysteine (SAH) to form S-methyl-5'-thioribose (MTR) and S-ribosyl-L-homocysteine (SRH), respectively. The MTANs are involved in quorum sensing pathways and hydrolyze MTA to metabolites for recycling to S-adenosylmethionine (SAM). A few bacterial species use the futalosine pathway for menaquinone synthesis and in these, MTAN catalyzes an essential step, making it a candidate for species-specific antibiotic development. Helicobacter pylori uses the unusual futalosine pathway for menaquinone biosynthesis and the MTAN from H. pylori (HpMTAN) is a target for antibiotic development. Human 5'-methylthioadenosine phosphorylase (MTAP) catalyzes phosphorylation reactions with substrate specificity similar to the bacterial MTANs. It plays a metabolic role in the salvage of MTA for SAM salvage pathways and has been reported to be an anticancer target. Transition state analogues designed for HpMTAN and for MTAP have been reported and show significant overlap in specificity. It is desirable to design transition state analogues specific for the HpMTAN as an antibiotic in the treatment of H. pylori infections. Fifteen unique transition state analogues are described here and are used to explore the inhibitor specificity and the structural scaffolds for HpMTAN and MTAP. Several inhibitors are transition-state analogues of H. pylori MTAN with dissociation constants in the picomolar range while inhibiting human MTAP with orders of magnitude weaker affinity. X-ray crystal structures of HpMTAN and MTAP show inhibitors of HpMTAN extending through a hydrophobic channel to the protein surface, while the more enclosed catalytic sites of human MTAP require the inhibitors to adopt a folded structure, displacing the catalytic site phosphate nucleophile.

-	~~Authors: Harijan, R~~.K., Ducati, ~~R.G.~~, ~~Bonanno~~, J.B.~~, Almo, S~~.C.~~, Schramm, V~~.L.	+	"Selective inhibitors of H. pylori methylthioadenosine nucleosidase and human methylthioadenosine phosphorylase".,Harijan RK, Hoff O, Ducati RG, Firestone RS, Hirsch BM, Evans GB, Schramm VL, Tyler PC J Med Chem. 2019 Mar 12. doi: 10.1021/acs.jmedchem.8b01642. PMID:30860833<ref>PMID:30860833</ref>

-	~~Description: Crystal structure of Helicobacter pylori 5'-methylthioadenosine~~/~~S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R~~,~~4S)-1-((4~~-~~amino~~-~~5H-pyrrolo~~[~~3,2-d~~]~~pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Almo, S.C]]	+	<div class="pdbe-citations 6dyv" style="background-color:#fffaf0;"></div>
-	[[Category: Ducati, R.G]]	+	== References ==
-	[[Category: Schramm, V.L]]	+	<references/>
-	[[Category: ~~Bonanno, J.B~~]]	+	__TOC__
-	[[Category: ~~Harijan, R.K~~]]	+	</StructureSection>
		+	[[Category: Adenosylhomocysteine nucleosidase]]
		+	[[Category: Large Structures]]
		+	[[Category: Almo, S C]]
		+	[[Category: Bonanno, J B]]
		+	[[Category: Ducati, R G]]
		+	[[Category: Harijan, R K]]
		+	[[Category: Schramm, V L]]
		+	[[Category: Duodenal ulcer]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Mtan enzyme]]
		+	[[Category: Stomach cancer]]

OCA at 05:28, 18 July 2018

OCA — Wed, 18 Jul 2018 05:28:22 GMT

←Older revision		Revision as of 05:28, 18 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Harijan, R.K., Ducati, R.G., Bonanno, J.B., Almo, S.C., Schramm, V.L.		Authors: Harijan, R.K., Ducati, R.G., Bonanno, J.B., Almo, S.C., Schramm, V.L.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Almo, S.C]]		[[Category: Almo, S.C]]
		+	[[Category: Ducati, R.G]]
	[[Category: Schramm, V.L]]		[[Category: Schramm, V.L]]
-	[[Category: Harijan, R.K]]
	[[Category: Bonanno, J.B]]		[[Category: Bonanno, J.B]]
-	[[Category: ~~Ducati~~, R.G]]	+	[[Category: Harijan, R.K]]

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

OCA — Wed, 11 Jul 2018 04:08:13 GMT

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

←Older revision

Revision as of 04:08, 11 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dyv is ON HOLD Authors: Harijan, R.K., Ducati, R.G., Bonanno, J.B., Almo, S.C., Schramm, V.L. Description: Crystal structure of Helicobacter pylor...

OCA — Wed, 11 Jul 2018 04:08:12 GMT

New page: '''Unreleased structure''' The entry 6dyv is ON HOLD Authors: Harijan, R.K., Ducati, R.G., Bonanno, J.B., Almo, S.C., Schramm, V.L. Description: Crystal structure of Helicobacter pylor...

New page

'''Unreleased structure'''

The entry 6dyv is ON HOLD

Authors: Harijan, R.K., Ducati, R.G., Bonanno, J.B., Almo, S.C., Schramm, V.L.

Description: Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol
[[Category: Unreleased Structures]]
[[Category: Almo, S.C]]
[[Category: Schramm, V.L]]
[[Category: Harijan, R.K]]
[[Category: Bonanno, J.B]]
[[Category: Ducati, R.G]]