6czl - Revision history

OCA at 14:31, 13 March 2024

2024-03-13T14:31:42Z

←Older revision		Revision as of 14:31, 13 March 2024
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	==Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form==		==Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form==
-	<StructureSection load='6czl' size='340' side='right' caption='[[6czl]], [[Resolution\|resolution]] 2.92Å' scene=''>	+	<StructureSection load='6czl' size='340' side='right'caption='[[6czl]], [[Resolution\|resolution]] 2.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6czl]] is a 6 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=6CZL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6czl]] is a 6 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=6CZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CZL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.92Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~11438625, MTR_4g130680 ([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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=6czl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czl OCA], [~~http~~://pdbe.org/6czl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6czl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6czl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6czl 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=6czl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czl OCA], [https://pdbe.org/6czl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6czl RCSB], [https://www.ebi.ac.uk/pdbsum/6czl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6czl ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/G7JFL4_MEDTR G7JFL4_MEDTR]
-	In the first committed step of histidine biosynthesis, ATP and 5-phosphoribosyl-alpha1-pyrophosphate (PRPP), in a presence of ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17), yield phosphoribosyl-ATP. ATP-PRTs are subject to feedback inhibition by histidine, that allosterically binds between the regulatory domains. Histidine biosynthetic pathways of bacteria, lower eukaryotes, and plants are considered promising targets for a design of antibiotics, antifungal agents, and herbicides because higher organisms are histidine heterotrophs. Plant ATP-PRTs are similar to one of the two types of their bacterial counterparts, the long-type ATP-PRTs. A biochemical and structural study of ATP-PRT from the model legume plant, Medicago truncatula ( Medtr ATP-PRT1) is reported herein. Two crystal structures, presenting homohexameric Medtr ATP-PRT1 in its relaxed (R-) and histidine-bound, tense (T-) states allowed to observe key features of the enzyme and provided the first structural insights into an ATP-PRT from a eukaryotic organism. In particular, they show pronounced conformational reorganizations during R-state to T-state transition that involves substantial movements of domains. This rearrangement requires a trans - to cis - switch of a peptide backbone within the hinge region of Medtr ATP-PRT1. A C-terminal alpha-helix, absent in bacteria, reinforces the hinge that is constituted by two peptide strands. As a result, conformations of the R- and T-states are significantly different from the corresponding states of prokaryotic enzymes with known 3-D structures. ~~Lastly, AMP bound at the active site is consistent with a competitive (and synergistic with histidine) nature of AMP inhibition~~.	+

-	Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states.,Ruszkowski M Biochem J. 2018 Aug 2. pii: BCJ20180289. doi: 10.1042/BCJ20180289. PMID:30072492<ref>PMID:30072492</ref>	+	==See Also==
-		+	*[[ATP phosphoribosyl transferase 3D structures\|ATP phosphoribosyl transferase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6czl" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Barrel medic~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ruszkowski, M~~]]	+	[[Category: Medicago truncatula]]
-	[[Category: ~~Allosteric regulation]]~~	+	[[Category: Ruszkowski M]]
-	~~[[Category: Atp-prt]]~~	+
-	~~[[Category: Histidine biosynthesis]]~~	+
-	~~[[Category: Prpp]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:51, 12 September 2018

2018-09-12T07:51:26Z

←Older revision		Revision as of 07:51, 12 September 2018
Line 3:		Line 3:
	<StructureSection load='6czl' size='340' side='right' caption='[[6czl]], [[Resolution\|resolution]] 2.92Å' scene=''>		<StructureSection load='6czl' size='340' side='right' caption='[[6czl]], [[Resolution\|resolution]] 2.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6czl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6czl]] is a 6 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=6CZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">11438625, MTR_4g130680 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</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=6czl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czl OCA], [http://pdbe.org/6czl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czl RCSB], [http://www.ebi.ac.uk/pdbsum/6czl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czl 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=6czl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czl OCA], [http://pdbe.org/6czl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czl RCSB], [http://www.ebi.ac.uk/pdbsum/6czl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czl ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Barrel medic]]
	[[Category: Ruszkowski, M]]		[[Category: Ruszkowski, M]]
	[[Category: Allosteric regulation]]		[[Category: Allosteric regulation]]

OCA at 16:15, 15 August 2018

2018-08-15T16:15:25Z

←Older revision		Revision as of 16:15, 15 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6czl is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form==
		+	<StructureSection load='6czl' size='340' side='right' caption='[[6czl]], [[Resolution\|resolution]] 2.92Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6czl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=6czl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czl OCA], [http://pdbe.org/6czl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czl RCSB], [http://www.ebi.ac.uk/pdbsum/6czl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the first committed step of histidine biosynthesis, ATP and 5-phosphoribosyl-alpha1-pyrophosphate (PRPP), in a presence of ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17), yield phosphoribosyl-ATP. ATP-PRTs are subject to feedback inhibition by histidine, that allosterically binds between the regulatory domains. Histidine biosynthetic pathways of bacteria, lower eukaryotes, and plants are considered promising targets for a design of antibiotics, antifungal agents, and herbicides because higher organisms are histidine heterotrophs. Plant ATP-PRTs are similar to one of the two types of their bacterial counterparts, the long-type ATP-PRTs. A biochemical and structural study of ATP-PRT from the model legume plant, Medicago truncatula ( Medtr ATP-PRT1) is reported herein. Two crystal structures, presenting homohexameric Medtr ATP-PRT1 in its relaxed (R-) and histidine-bound, tense (T-) states allowed to observe key features of the enzyme and provided the first structural insights into an ATP-PRT from a eukaryotic organism. In particular, they show pronounced conformational reorganizations during R-state to T-state transition that involves substantial movements of domains. This rearrangement requires a trans - to cis - switch of a peptide backbone within the hinge region of Medtr ATP-PRT1. A C-terminal alpha-helix, absent in bacteria, reinforces the hinge that is constituted by two peptide strands. As a result, conformations of the R- and T-states are significantly different from the corresponding states of prokaryotic enzymes with known 3-D structures. Lastly, AMP bound at the active site is consistent with a competitive (and synergistic with histidine) nature of AMP inhibition.

-	~~Authors~~: ~~Ruszkowski~~, M.	+	Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states.,Ruszkowski M Biochem J. 2018 Aug 2. pii: BCJ20180289. doi: 10.1042/BCJ20180289. PMID:30072492<ref>PMID:30072492</ref>

-	~~Description: Crystal structure~~ of ~~Medicago truncatula ATP-phosphoribosyltransferase in relaxed form~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 6czl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Ruszkowski, M]]		[[Category: Ruszkowski, M]]
		+	[[Category: Allosteric regulation]]
		+	[[Category: Atp-prt]]
		+	[[Category: Histidine biosynthesis]]
		+	[[Category: Prpp]]
		+	[[Category: Transferase]]

OCA at 06:39, 2 May 2018

2018-05-02T06:39:54Z

←Older revision		Revision as of 06:39, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Ruszkowski, M.		Authors: Ruszkowski, M.

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

2018-04-18T04:15:46Z

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

←Older revision

Revision as of 04:15, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6czl is ON HOLD Authors: Ruszkowski, M. Description: Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form [[Categ...

2018-04-18T04:15:44Z

New page: '''Unreleased structure''' The entry 6czl is ON HOLD Authors: Ruszkowski, M. Description: Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form [[Categ...

New page

'''Unreleased structure'''

The entry 6czl is ON HOLD

Authors: Ruszkowski, M.

Description: Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form
[[Category: Unreleased Structures]]
[[Category: Ruszkowski, M]]