4nme - Revision history

OCA at 16:59, 20 September 2023

OCA — Wed, 20 Sep 2023 16:59:55 GMT

←Older revision		Revision as of 16:59, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacter_sulfurreducens_PCA Geobacter sulfurreducens PCA]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NME FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacter_sulfurreducens_PCA Geobacter sulfurreducens PCA]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NME FirstGlance]. <br>
-	</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=P5F:N-PROPARGYLGLYCINE-MODIFIED+FLAVIN+ADENINE+DINUCLEOTIDE'>P5F</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]] 2.088Å</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=P5F:N-PROPARGYLGLYCINE-MODIFIED+FLAVIN+ADENINE+DINUCLEOTIDE'>P5F</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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [https://pdbe.org/4nme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [https://www.ebi.ac.uk/pdbsum/4nme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nme 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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [https://pdbe.org/4nme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [https://www.ebi.ac.uk/pdbsum/4nme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nme ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:34, 11 January 2023

OCA — Wed, 11 Jan 2023 08:34:39 GMT

←Older revision		Revision as of 08:34, 11 January 2023
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	==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine==		==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine==
-	<StructureSection load='4nme' size='340' side='right' caption='[[4nme]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='4nme' size='340' side='right'caption='[[4nme]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nme]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geosl Geosl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacter_sulfurreducens_PCA Geobacter sulfurreducens PCA]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NME 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=P5F:N-PROPARGYLGLYCINE-MODIFIED+FLAVIN+ADENINE+DINUCLEOTIDE'>P5F</scene>~~</td></tr>~~	+	</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=P5F:N-PROPARGYLGLYCINE-MODIFIED+FLAVIN+ADENINE+DINUCLEOTIDE'>P5F</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nm9\|4nm9]], [[4nma\|4nma]], [[4nmb\|4nmb]], [[4nmc\|4nmc]], [[4nmd\|4nmd]], [[4nmf\|4nmf]]</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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [https://pdbe.org/4nme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [https://www.ebi.ac.uk/pdbsum/4nme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nme ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">putA, GSU3395 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243231 GEOSL])~~</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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [~~http~~://pdbe.org/4nme PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nme PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nme ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q746X3_GEOSL Q746X3_GEOSL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geosl~~]]	+	[[Category: Geobacter sulfurreducens PCA]]
-	[[Category: ~~Singh, H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Tanner, J J~~]]	+	[[Category: Singh H]]
-	[[Category: ~~Aldehyde dehydrogenase]]~~	+	[[Category: Tanner JJ]]
-	~~[[Category: Bifunctional enzyme]]~~	+
-	~~[[Category: Flavin adenine dinucleotide]]~~	+
-	~~[[Category: Flavoenzyme]]~~	+
-	~~[[Category: Mechanism-based inactivation]]~~	+
-	~~[[Category: Nicotinamide adenine dinucleotide]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Proline catabolism]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Substrate channeling~~]]	+

OCA at 18:20, 11 August 2016

OCA — Thu, 11 Aug 2016 18:20:05 GMT

←Older revision		Revision as of 18:20, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine==		==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine==
	<StructureSection load='4nme' size='340' side='right' caption='[[4nme]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='4nme' size='340' side='right' caption='[[4nme]], [[Resolution\|resolution]] 2.09Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nm9\|4nm9]], [[4nma\|4nma]], [[4nmb\|4nmb]], [[4nmc\|4nmc]], [[4nmd\|4nmd]], [[4nmf\|4nmf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nm9\|4nm9]], [[4nma\|4nma]], [[4nmb\|4nmb]], [[4nmc\|4nmc]], [[4nmd\|4nmd]], [[4nmf\|4nmf]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">putA, GSU3395 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243231 GEOSL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">putA, GSU3395 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243231 GEOSL])</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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [http://www.ebi.ac.uk/pdbsum/4nme PDBsum]</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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [http://pdbe.org/4nme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [http://www.ebi.ac.uk/pdbsum/4nme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nme ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4nme" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proline utilization A\|Proline utilization A]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:00, 5 January 2015

OCA — Mon, 05 Jan 2015 09:00:56 GMT

←Older revision		Revision as of 09:00, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4nme\| PDB=4nme \| SCENE= }}~~	+	==Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine==
-	===Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine===	+	<StructureSection load='4nme' size='340' side='right' caption='[[4nme]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24550478}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4nme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geosl Geosl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NME 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=P5F:N-PROPARGYLGLYCINE-MODIFIED+FLAVIN+ADENINE+DINUCLEOTIDE'>P5F</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nm9\|4nm9]], [[4nma\|4nma]], [[4nmb\|4nmb]], [[4nmc\|4nmc]], [[4nmd\|4nmd]], [[4nmf\|4nmf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">putA, GSU3395 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243231 GEOSL])</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=4nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nme RCSB], [http://www.ebi.ac.uk/pdbsum/4nme PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proline utilization A (PutA) proteins are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of l-proline to l-glutamate by the sequential activities of proline dehydrogenase and aldehyde dehydrogenase domains. Located at the inner membrane of Gram-negative bacteria, PutAs play a major role in energy metabolism by coupling the oxidation of proline imported from the environment to the reduction of membrane-associated quinones. Here, we report seven crystal structures of the 1,004-residue PutA from Geobacter sulfurreducens, along with determination of the protein oligomeric state by small-angle X-ray scattering and kinetic characterization of substrate channeling and quinone reduction. The structures reveal an elaborate and dynamic tunnel system featuring a 75-A-long tunnel that links the two active sites and six smaller tunnels that connect the main tunnel to the bulk medium. The locations of these tunnels and their responses to ligand binding and flavin reduction suggest hypotheses about how proline, water, and quinones enter the tunnel system and where l-glutamate exits. Kinetic measurements show that glutamate production from proline occurs without a lag phase, consistent with substrate channeling and implying that the observed tunnel is functionally relevant. Furthermore, the structure of reduced PutA complexed with menadione bisulfite reveals the elusive quinone-binding site. The benzoquinone binds within 4.0 A of the flavin si face, consistent with direct electron transfer. The location of the quinone site implies that the concave surface of the PutA dimer approaches the membrane. Altogether, these results provide insight into how PutAs couple proline oxidation to quinone reduction.

-	~~==About this Structure==~~	+	Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.,Singh H, Arentson BW, Becker DF, Tanner JJ Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3389-94. doi:, 10.1073/pnas.1321621111. Epub 2014 Feb 18. PMID:24550478<ref>PMID:24550478</ref>
-	~~[[4nme]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4NME OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024550478</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Singh, H.]]	+	== References ==
-	[[Category: Tanner, J J.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Geosl]]
		+	[[Category: Singh, H]]
		+	[[Category: Tanner, J J]]
	[[Category: Aldehyde dehydrogenase]]		[[Category: Aldehyde dehydrogenase]]
	[[Category: Bifunctional enzyme]]		[[Category: Bifunctional enzyme]]

OCA at 09:17, 19 March 2014

OCA — Wed, 19 Mar 2014 09:17:31 GMT

←Older revision		Revision as of 09:17, 19 March 2014
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	{{STRUCTURE_4nme\| PDB=4nme \| SCENE= }}		{{STRUCTURE_4nme\| PDB=4nme \| SCENE= }}
	===Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine===		===Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine===
		+	{{ABSTRACT_PUBMED_24550478}}

	==About this Structure==		==About this Structure==
	[[4nme]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA].		[[4nme]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024550478</ref><references group="xtra"/><references/>
	[[Category: Singh, H.]]		[[Category: Singh, H.]]
	[[Category: Tanner, J J.]]		[[Category: Tanner, J J.]]

OCA at 17:55, 19 February 2014

OCA — Wed, 19 Feb 2014 17:55:31 GMT

←Older revision		Revision as of 17:55, 19 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nme\| PDB=4nme \| SCENE= }}
		+	===Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine===

-	~~The entry~~ 4nme is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4nme]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NME OCA].
-	~~Authors~~: Singh, H., Tanner, J.J.	+	[[Category: Singh, H.]]
-		+	[[Category: Tanner, J J.]]
-	~~Description~~: ~~Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N~~-~~propargylglycine~~	+	[[Category: Aldehyde dehydrogenase]]
		+	[[Category: Bifunctional enzyme]]
		+	[[Category: Flavin adenine dinucleotide]]
		+	[[Category: Flavoenzyme]]
		+	[[Category: Mechanism-based inactivation]]
		+	[[Category: Nicotinamide adenine dinucleotide]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Proline catabolism]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Substrate channeling]]

OCA at 09:25, 25 December 2013

OCA — Wed, 25 Dec 2013 09:25:04 GMT

←Older revision		Revision as of 09:25, 25 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nme is ON HOLD	+	The entry 4nme is ON HOLD until Paper Publication

	Authors: Singh, H., Tanner, J.J.		Authors: Singh, H., Tanner, J.J.

	Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine		Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine

OCA at 06:50, 4 December 2013

OCA — Wed, 04 Dec 2013 06:50:40 GMT

←Older revision		Revision as of 06:50, 4 December 2013
Line 3:		Line 3:
	The entry 4nme is ON HOLD		The entry 4nme is ON HOLD

-	Authors: Singh, ~~Harkewal~~, Tanner, ~~John~~ J.	+	Authors: Singh, H., Tanner, J.J.

	Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine		Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine

OCA: Protected "4nme" [edit=sysop:move=sysop]

OCA — Wed, 20 Nov 2013 13:03:15 GMT

Protected "4nme" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:03, 20 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nme is ON HOLD Authors: Singh, Harkewal, Tanner, John J. Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreduc...

OCA — Wed, 20 Nov 2013 13:03:14 GMT

New page: '''Unreleased structure''' The entry 4nme is ON HOLD Authors: Singh, Harkewal, Tanner, John J. Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreduc...

New page

'''Unreleased structure'''

The entry 4nme is ON HOLD

Authors: Singh, Harkewal, Tanner, John J.

Description: Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine