6r02 - Revision history

OCA at 12:12, 24 January 2024

2024-01-24T12:12:20Z

←Older revision		Revision as of 12:12, 24 January 2024
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	<StructureSection load='6r02' size='340' side='right'caption='[[6r02]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6r02' size='340' side='right'caption='[[6r02]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r02]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R02 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r02]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychrobacter_arcticus Psychrobacter arcticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R02 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=HIS:HISTIDINE'>HIS</scene~~>, ~~<scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</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]] 2.65Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/ATP_phosphoribosyltransferase ATP phosphoribosyltransferase]~~, ~~with EC number [http~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.4.2.17 2.4.2.17]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HIS:HISTIDINE'>HIS</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</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=6r02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r02 OCA], [~~http~~://pdbe.org/6r02 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r02 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r02 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r02 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=6r02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r02 OCA], [https://pdbe.org/6r02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r02 RCSB], [https://www.ebi.ac.uk/pdbsum/6r02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r02 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/HISZ_PSYA2 HISZ_PSYA2]] Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine.[HAMAP-Rule:MF_00125] [[http://www.uniprot.org/uniprot/HIS1_PSYA2 HIS1_PSYA2]] Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity.	+	[https://www.uniprot.org/uniprot/HIS1_PSYA2 HIS1_PSYA2] Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6r02" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6r02" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ATP phosphoribosyl transferase 3D structures\|ATP phosphoribosyl transferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ATP phosphoribosyltransferase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Alphey, M S~~]]	+	[[Category: Psychrobacter arcticus]]
-	[[Category: ~~Silva, R G.da~~]]	+	[[Category: Alphey MS]]
-	[[Category: Thomson~~, C M~~]]	+	[[Category: Thomson CM]]
-	[[Category: ~~Atpprt]]~~	+	[[Category: Da Silva RG]]
-	~~[[Category: Histidine]]~~	+
-	~~[[Category: Phosphoribosyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:04, 7 August 2019

2019-08-07T06:04:16Z

←Older revision		Revision as of 06:04, 7 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6r02 is ~~ON HOLD until Paper~~ Publication	+	==Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and PRPP==
		+	<StructureSection load='6r02' size='340' side='right'caption='[[6r02]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r02]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R02 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIS:HISTIDINE'>HIS</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP_phosphoribosyltransferase ATP phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.17 2.4.2.17] </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=6r02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r02 OCA], [http://pdbe.org/6r02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r02 RCSB], [http://www.ebi.ac.uk/pdbsum/6r02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r02 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HISZ_PSYA2 HISZ_PSYA2]] Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine.[HAMAP-Rule:MF_00125] [[http://www.uniprot.org/uniprot/HIS1_PSYA2 HIS1_PSYA2]] Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ATP phosphoribosyltransferase (ATPPRT) catalyzes the first step of histidine biosynthesis, being allosterically inhibited by the final product of the pathway. Allosteric inhibition of long-form ATPPRTs by histidine has been extensively studied, but inhibition of short-form ATPPRTs is poorly understood. Short-form ATPPRTs are hetero-octamers formed by four catalytic subunits (HisGS) and four regulatory subunits (HisZ). HisGS alone is catalytically active and insensitive to histidine. HisZ enhances catalysis by HisGS in the absence of histidine but mediates allosteric inhibition in its presence. Here, steady-state and pre-steady-state kinetics establish that histidine is a noncompetitive inhibitor of short-form ATPPRT and that inhibition does not occur by dissociating HisGS from the hetero-octamer. The crystal structure of ATPPRT in complex with histidine and the substrate 5-phospho-alpha-d-ribosyl-1-pyrophosphate was determined, showing histidine bound solely to HisZ, with four histidine molecules per hetero-octamer. Histidine binding involves the repositioning of two HisZ loops. The histidine-binding loop moves closer to histidine to establish polar contacts. This leads to a hydrogen bond between its Tyr263 and His104 in the Asp101-Leu117 loop. The Asp101-Leu117 loop leads to the HisZ-HisGS interface, and in the absence of histidine, its motion prompts HisGS conformational changes responsible for catalytic activation. Following histidine binding, interaction with the histidine-binding loop may prevent the Asp101-Leu117 loop from efficiently sampling conformations conducive to catalytic activation. Tyr263Phe-PaHisZ-containing PaATPPRT, however, is less susceptible though not insensitive to histidine inhibition, suggesting the Tyr263-His104 interaction may be relevant to yet not solely responsible for transmission of the allosteric signal.

-	~~Authors:~~ Alphey, ~~M.S.~~, da Silva~~, R~~.G.~~, Thomson, C~~.M.	+	Mapping the Structural Path for Allosteric Inhibition of a Short-Form ATP Phosphoribosyltransferase by Histidine.,Thomson CM, Alphey MS, Fisher G, da Silva RG Biochemistry. 2019 Jul 16;58(28):3078-3086. doi: 10.1021/acs.biochem.9b00282., Epub 2019 Jun 28. PMID:31251578<ref>PMID:31251578</ref>

-	~~Description~~: ~~Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and PRPP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Thomson, C.M~~]]	+	<div class="pdbe-citations 6r02" style="background-color:#fffaf0;"></div>
-	[[Category: Alphey, M.S]]	+	== References ==
-	[[Category: Da Silva, R.G]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: ATP phosphoribosyltransferase]]
		+	[[Category: Large Structures]]
		+	[[Category: Alphey, M S]]
		+	[[Category: Silva, R G.da]]
		+	[[Category: Thomson, C M]]
		+	[[Category: Atpprt]]
		+	[[Category: Histidine]]
		+	[[Category: Phosphoribosyltransferase]]
		+	[[Category: Transferase]]

OCA at 05:10, 27 March 2019

2019-03-27T05:10:24Z

←Older revision		Revision as of 05:10, 27 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6r02 is ON HOLD	+	The entry 6r02 is ON HOLD until Paper Publication

	Authors: Alphey, M.S., da Silva, R.G., Thomson, C.M.		Authors: Alphey, M.S., da Silva, R.G., Thomson, C.M.

OCA: Protected "6r02" [edit=sysop:move=sysop]

2019-03-20T06:14:01Z

Protected "6r02" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:14, 20 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r02 is ON HOLD Authors: Alphey, M.S., da Silva, R.G., Thomson, C.M. Description: Psychrobacter arcticus ATP phosphoribosyltransferase bound to his...

2019-03-20T06:13:59Z

New page: '''Unreleased structure''' The entry 6r02 is ON HOLD Authors: Alphey, M.S., da Silva, R.G., Thomson, C.M. Description: Psychrobacter arcticus ATP phosphoribosyltransferase bound to his...

New page

'''Unreleased structure'''

The entry 6r02 is ON HOLD

Authors: Alphey, M.S., da Silva, R.G., Thomson, C.M.

Description: Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and PRPP
[[Category: Unreleased Structures]]
[[Category: Thomson, C.M]]
[[Category: Alphey, M.S]]
[[Category: Da Silva, R.G]]