5b7p - Revision history

OCA at 09:07, 20 March 2024

OCA — Wed, 20 Mar 2024 09:07:49 GMT

←Older revision		Revision as of 09:07, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeromonas_hydrophila_subsp._hydrophila_ATCC_7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeromonas_hydrophila_subsp._hydrophila_ATCC_7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B7P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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]] 1.49Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [https://pdbe.org/5b7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [https://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p 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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [https://pdbe.org/5b7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [https://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0KGU9_AERHH A0KGU9_AERHH]		[https://www.uniprot.org/uniprot/A0KGU9_AERHH A0KGU9_AERHH]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Gram-negative, rod-shaped bacterium Aeromonas hydrophila has two multifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzymes, MtaN-1 and MtaN-2, that differ from those in other bacteria. These proteins are essential for several metabolic pathways, including biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing. To gain insight into how these two proteins function, we determined four high-resolution crystal structures of MtaN-1 in its apo form and in complex with the substrates S-adenosyl-l-homocysteine, 5'-methylthioadenosine, and 5'-deoxyadenosine. We found that the domain structures were generally similar, although slight differences were evident. The crystal structure demonstrates that AhMtaN-1 has an extension of the binding pocket and revealed that a tryptophan in the active site (Trp199) may play a major role in substrate binding, unlike in other MTAN proteins. Mutation of the Trp199 residue completely abolished the enzyme activity. Trp199 was identified as an active site residue that is essential for catalysis. Furthermore, biochemical characterization of AhMtaN-1 and AhMtaN-2 demonstrated that AhMtaN-1 exhibits inherent trypsin resistance that is higher than that of AhMtaN-2. Additionally, the thermally unfolded AhMtaN-2 protein is capable of refolding into active forms, whereas the thermally unfolded AhMtaN-1 protein does not have this ability. Examining the different biochemical characteristics related to the functional roles of AhMtaN-1 and AhMtaN-2 would be interesting. Indeed, the biochemical characterization of these structural features would provide a structural basis for the design of new antibiotics against A. hydrophila.
-
-	Structural and Functional Analyses of Periplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase from Aeromonas hydrophila.,Xu Y, Wang L, Chen J, Zhao J, Fan S, Dong Y, Ha NC, Quan C Biochemistry. 2017 Oct 10;56(40):5347-5355. doi: 10.1021/acs.biochem.7b00691., Epub 2017 Sep 20. PMID:28862845<ref>PMID:28862845</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5b7p" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:41, 31 May 2023

OCA — Wed, 31 May 2023 06:41:16 GMT

←Older revision		Revision as of 06:41, 31 May 2023
Line 1:		Line 1:

	==Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila==		==Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila==
-	<StructureSection load='5b7p' size='340' side='right' caption='[[5b7p]], [[Resolution\|resolution]] 1.49Å' scene=''>	+	<StructureSection load='5b7p' size='340' side='right'caption='[[5b7p]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aerhh Aerhh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeromonas_hydrophila_subsp._hydrophila_ATCC_7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B7P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b7n\|5b7n]], [[5b7q\|5b7q]]</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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [https://pdbe.org/5b7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [https://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnN-1, AHA_0953 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380703 AERHH])~~</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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [~~http~~://pdbe.org/5b7p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0KGU9_AERHH A0KGU9_AERHH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Aerhh]]~~	+	[[Category: Aeromonas hydrophila subsp. hydrophila ATCC 7966]]
-	~~[[Category: Xu, Y]]~~	+	[[Category: Large Structures]]
-	~~[[Category: 5-dao]]~~	+	[[Category: Xu Y]]
-	[[Category: Aeromonas hydrophila]]	+
-	[[Category: ~~Hydrolase~~]]	+
-	[[Category: ~~Mta]]~~	+
-	~~[[Category: Mtan-1]]~~	+
-	~~[[Category: Mtan-2]]~~	+
-	~~[[Category: Sah~~]]	+

OCA at 07:21, 13 December 2017

OCA — Wed, 13 Dec 2017 07:21:35 GMT

←Older revision		Revision as of 07:21, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5b7p' size='340' side='right' caption='[[5b7p]], [[Resolution\|resolution]] 1.49Å' scene=''>		<StructureSection load='5b7p' size='340' side='right' caption='[[5b7p]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerhh Aerhh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B7P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b7n\|5b7n]], [[5b7q\|5b7q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b7n\|5b7n]], [[5b7q\|5b7q]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnN-1, AHA_0953 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380703 AERHH])</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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [http://pdbe.org/5b7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [http://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p 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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [http://pdbe.org/5b7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [http://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Gram-negative, rod-shaped bacterium Aeromonas hydrophila has two multifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzymes, MtaN-1 and MtaN-2, that differ from those in other bacteria. These proteins are essential for several metabolic pathways, including biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing. To gain insight into how these two proteins function, we determined four high-resolution crystal structures of MtaN-1 in its apo form and in complex with the substrates S-adenosyl-l-homocysteine, 5'-methylthioadenosine, and 5'-deoxyadenosine. We found that the domain structures were generally similar, although slight differences were evident. The crystal structure demonstrates that AhMtaN-1 has an extension of the binding pocket and revealed that a tryptophan in the active site (Trp199) may play a major role in substrate binding, unlike in other MTAN proteins. Mutation of the Trp199 residue completely abolished the enzyme activity. Trp199 was identified as an active site residue that is essential for catalysis. Furthermore, biochemical characterization of AhMtaN-1 and AhMtaN-2 demonstrated that AhMtaN-1 exhibits inherent trypsin resistance that is higher than that of AhMtaN-2. Additionally, the thermally unfolded AhMtaN-2 protein is capable of refolding into active forms, whereas the thermally unfolded AhMtaN-1 protein does not have this ability. Examining the different biochemical characteristics related to the functional roles of AhMtaN-1 and AhMtaN-2 would be interesting. Indeed, the biochemical characterization of these structural features would provide a structural basis for the design of new antibiotics against A. hydrophila.
		+
		+	Structural and Functional Analyses of Periplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase from Aeromonas hydrophila.,Xu Y, Wang L, Chen J, Zhao J, Fan S, Dong Y, Ha NC, Quan C Biochemistry. 2017 Oct 10;56(40):5347-5355. doi: 10.1021/acs.biochem.7b00691., Epub 2017 Sep 20. PMID:28862845<ref>PMID:28862845</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5b7p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aerhh]]
	[[Category: Xu, Y]]		[[Category: Xu, Y]]
	[[Category: 5-dao]]		[[Category: 5-dao]]

OCA at 19:12, 15 December 2016

OCA — Thu, 15 Dec 2016 19:12:37 GMT

←Older revision		Revision as of 19:12, 15 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5b7p is ON HOLD until Dec 08 2017~~	+	==Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila==
-		+	<StructureSection load='5b7p' size='340' side='right' caption='[[5b7p]], [[Resolution\|resolution]] 1.49Å' scene=''>
-	~~Authors: Xu, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5b7p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B7P FirstGlance]. <br>
-	~~Description:~~ Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b7n\|5b7n]], [[5b7q\|5b7q]]</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=5b7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b7p OCA], [http://pdbe.org/5b7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b7p RCSB], [http://www.ebi.ac.uk/pdbsum/5b7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b7p ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Xu, Y]]		[[Category: Xu, Y]]
		+	[[Category: 5-dao]]
		+	[[Category: Aeromonas hydrophila]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mta]]
		+	[[Category: Mtan-1]]
		+	[[Category: Mtan-2]]
		+	[[Category: Sah]]

OCA at 07:10, 21 September 2016

OCA — Wed, 21 Sep 2016 07:10:12 GMT

←Older revision		Revision as of 07:10, 21 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5b7p is ON HOLD	+	The entry 5b7p is ON HOLD until Dec 08 2017

	Authors: Xu, Y.		Authors: Xu, Y.

OCA at 16:48, 23 June 2016

OCA — Thu, 23 Jun 2016 16:48:05 GMT

←Older revision		Revision as of 16:48, 23 June 2016
Line 3:		Line 3:
	The entry 5b7p is ON HOLD		The entry 5b7p is ON HOLD

-	Authors: ~~Yongbin~~ Xu	+	Authors: Xu, Y.

	Description: Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila		Description: Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Yongbin~~ Xu]]	+	[[Category: Xu, Y]]

OCA: Protected "5b7p" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 09:07:18 GMT

Protected "5b7p" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:07, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5b7p is ON HOLD Authors: Yongbin Xu Description: Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nuc...

OCA — Mon, 20 Jun 2016 09:07:17 GMT

New page: '''Unreleased structure''' The entry 5b7p is ON HOLD Authors: Yongbin Xu Description: Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nuc...

New page

'''Unreleased structure'''

The entry 5b7p is ON HOLD

Authors: Yongbin Xu

Description: Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila
[[Category: Unreleased Structures]]
[[Category: Yongbin Xu]]