6nic - Revision history

OCA at 06:54, 11 October 2023

OCA — Wed, 11 Oct 2023 06:54:17 GMT

←Older revision		Revision as of 06:54, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6nic' size='340' side='right'caption='[[6nic]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nic' size='340' side='right'caption='[[6nic]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nic]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Barrel_medic Barrel medic~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NIC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NIC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nic]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Medicago_truncatula Medicago truncatula]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NIC 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=KQY:6-aminohexanamide'>KQY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.2Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">11445422, MTR_4g112810, MtrunA17_Chr4g0061951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</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=KQY:6-aminohexanamide'>KQY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=6nic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nic OCA], [https://pdbe.org/6nic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nic RCSB], [https://www.ebi.ac.uk/pdbsum/6nic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nic 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=6nic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nic OCA], [~~http~~://pdbe.org/6nic PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nic RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nic PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nic ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AGUA_MEDTR AGUA_MEDTR] Mediates the hydrolysis of agmatine into N-carbamoylputrescine in the arginine decarboxylase (ADC) pathway of putrescine biosynthesis, a basic polyamine.[UniProtKB:Q8GWW7]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Agmatine deiminase]]
-	[[Category: Barrel medic]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dauter, Z~~]]	+	[[Category: Medicago truncatula]]
-	[[Category: ~~Sekula, B~~]]	+	[[Category: Dauter Z]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Sekula B]]
-	~~[[Category: Polyamine metabolism]]~~	+
-	~~[[Category: Putrescine biosynthesis~~]]	+

OCA at 09:21, 1 May 2019

OCA — Wed, 01 May 2019 09:21:45 GMT

←Older revision		Revision as of 09:21, 1 May 2019
Line 3:		Line 3:
	<StructureSection load='6nic' size='340' side='right'caption='[[6nic]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nic' size='340' side='right'caption='[[6nic]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nic]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NIC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Barrel_medic Barrel medic]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NIC 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=KQY:6-aminohexanamide'>KQY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=KQY:6-aminohexanamide'>KQY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">11445422, MTR_4g112810, MtrunA17_Chr4g0061951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=6nic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nic OCA], [http://pdbe.org/6nic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nic RCSB], [http://www.ebi.ac.uk/pdbsum/6nic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nic 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=6nic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nic OCA], [http://pdbe.org/6nic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nic RCSB], [http://www.ebi.ac.uk/pdbsum/6nic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nic ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plants are unique eukaryotes that can produce putrescine (PUT), a basic diamine, from arginine via a three-step pathway. This process starts with arginine decarboxylase that converts arginine to agmatine. Then, the consecutive action of two hydrolytic enzymes, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase, ultimately produces PUT. An alternative route of PUT biosynthesis requires ornithine decarboxylase that catalyzes direct putrescine biosynthesis. However, some plant species lack this enzyme and rely only on agmatine pathway. The scope of this manuscript concerns the structural characterization of AIH from the model legume plant, Medicago truncatula. MtAIH is a homodimer built of two subunits with a characteristic propeller fold, where five alphabetabetaalphabeta repeated units are arranged around the fivefold pseudosymmetry axis. Dimeric assembly of this plant AIH, formed by interactions of conserved structural elements from one repeat, is drastically different from that observed in dimeric bacterial AIHs. Additionally, the structural snapshot of MtAIH in complex with 6-aminohexanamide, the reaction product analog, presents the conformation of the enzyme during catalysis. Our structural results show that MtAIH undergoes significant structural rearrangements of the long loop, which closes a tunnel-shaped active site over the course of the catalytic event. This conformational change is also observed in AIH from Arabidopsis thaliana, indicating the importance of the closed conformation of the gate-keeping loop for the catalysis of plant AIHs.
		+
		+	Structural Study of Agmatine Iminohydrolase From Medicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants.,Sekula B, Dauter Z Front Plant Sci. 2019 Mar 28;10:320. doi: 10.3389/fpls.2019.00320. eCollection, 2019. PMID:30984210<ref>PMID:30984210</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6nic" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
		+	[[Category: Barrel medic]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]

OCA at 08:03, 20 March 2019

OCA — Wed, 20 Mar 2019 08:03:30 GMT

←Older revision		Revision as of 08:03, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6nic is ON HOLD until Paper Publication~~	+	==Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide==
-		+	<StructureSection load='6nic' size='340' side='right'caption='[[6nic]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors: Sekula, B., Dauter, Z.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nic]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NIC FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide	+	</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=KQY:6-aminohexanamide'>KQY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=6nic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nic OCA], [http://pdbe.org/6nic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nic RCSB], [http://www.ebi.ac.uk/pdbsum/6nic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nic ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Agmatine deiminase]]
		+	[[Category: Large Structures]]
		+	[[Category: Dauter, Z]]
	[[Category: Sekula, B]]		[[Category: Sekula, B]]
-	[[Category: ~~Dauter, Z~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Polyamine metabolism]]
		+	[[Category: Putrescine biosynthesis]]

OCA at 06:31, 30 January 2019

OCA — Wed, 30 Jan 2019 06:31:42 GMT

←Older revision		Revision as of 06:31, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Sekula, B., Dauter, Z.		Authors: Sekula, B., Dauter, Z.

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

OCA — Wed, 02 Jan 2019 04:59:50 GMT

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

←Older revision

Revision as of 04:59, 2 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nic is ON HOLD Authors: Sekula, B., Dauter, Z. Description: Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Comple...

OCA — Wed, 02 Jan 2019 04:59:48 GMT

New page: '''Unreleased structure''' The entry 6nic is ON HOLD Authors: Sekula, B., Dauter, Z. Description: Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Comple...

New page

'''Unreleased structure'''

The entry 6nic is ON HOLD

Authors: Sekula, B., Dauter, Z.

Description: Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide
[[Category: Unreleased Structures]]
[[Category: Sekula, B]]
[[Category: Dauter, Z]]