8bqf - Revision history

OCA at 08:19, 7 February 2024

2024-02-07T08:19:29Z

←Older revision		Revision as of 08:19, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8bqf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[8bqf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</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]] 2.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</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=8bqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqf OCA], [https://pdbe.org/8bqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqf RCSB], [https://www.ebi.ac.uk/pdbsum/8bqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqf 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=8bqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqf OCA], [https://pdbe.org/8bqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqf RCSB], [https://www.ebi.ac.uk/pdbsum/8bqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/KAD_ECOLI KAD_ECOLI] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.[HAMAP-Rule:MF_00235]		[https://www.uniprot.org/uniprot/KAD_ECOLI KAD_ECOLI] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.[HAMAP-Rule:MF_00235]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Enzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. The mutation of multiple conserved residues reduces substrate inhibition, suggesting that substrate inhibition is an evolutionary well conserved feature in AK. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity.
-
-	Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase.,Scheerer D, Adkar BV, Bhattacharyya S, Levy D, Iljina M, Riven I, Dym O, Haran G, Shakhnovich EI Proc Natl Acad Sci U S A. 2023 May 2;120(18):e2219855120. doi: , 10.1073/pnas.2219855120. Epub 2023 Apr 24. PMID:37094144<ref>PMID:37094144</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8bqf" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:51, 10 May 2023

2023-05-10T06:51:55Z

←Older revision		Revision as of 06:51, 10 May 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8bqf is ~~ON HOLD until Paper~~ Publication	+	==Adenylate Kinase L107I MUTANT==
		+	<StructureSection load='8bqf' size='340' side='right'caption='[[8bqf]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8bqf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</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=8bqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqf OCA], [https://pdbe.org/8bqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqf RCSB], [https://www.ebi.ac.uk/pdbsum/8bqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KAD_ECOLI KAD_ECOLI] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.[HAMAP-Rule:MF_00235]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. The mutation of multiple conserved residues reduces substrate inhibition, suggesting that substrate inhibition is an evolutionary well conserved feature in AK. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity.

-	~~Authors:~~ Scheerer, D., Adkar~~, B.V.~~, Bhattacharyya, S., Levy, D., Iljina, M~~., Iljina~~, I., Dym, O., Haran, G., Shakhnovich, E.I.	+	Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase.,Scheerer D, Adkar BV, Bhattacharyya S, Levy D, Iljina M, Riven I, Dym O, Haran G, Shakhnovich EI Proc Natl Acad Sci U S A. 2023 May 2;120(18):e2219855120. doi: , 10.1073/pnas.2219855120. Epub 2023 Apr 24. PMID:37094144<ref>PMID:37094144</ref>

-	~~Description~~: ~~Adenylate Kinase L107I MUTANT~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Bhattacharyya, S~~]]	+	<div class="pdbe-citations 8bqf" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Iljina, I~~]]	+	== References ==
-	[[Category: ~~Haran, G~~]]	+	<references/>
-	[[Category: ~~Levy, D~~]]	+	__TOC__
-	[[Category: Iljina~~, M~~]]	+	</StructureSection>
-	[[Category: ~~Scheerer, D~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Dym, O~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Adkar, B.V~~]]	+	[[Category: Adkar BV]]
-	[[Category: Shakhnovich~~, E.I~~]]	+	[[Category: Bhattacharyya S]]
		+	[[Category: Dym O]]
		+	[[Category: Haran G]]
		+	[[Category: Iljina I]]
		+	[[Category: Iljina M]]
		+	[[Category: Levy D]]
		+	[[Category: Scheerer D]]
		+	[[Category: Shakhnovich EI]]

OCA at 05:27, 28 December 2022

2022-12-28T05:27:28Z

←Older revision		Revision as of 05:27, 28 December 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8bqf is ON HOLD	+	The entry 8bqf is ON HOLD until Paper Publication

	Authors: Scheerer, D., Adkar, B.V., Bhattacharyya, S., Levy, D., Iljina, M., Iljina, I., Dym, O., Haran, G., Shakhnovich, E.I.		Authors: Scheerer, D., Adkar, B.V., Bhattacharyya, S., Levy, D., Iljina, M., Iljina, I., Dym, O., Haran, G., Shakhnovich, E.I.
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	[[Category: Levy, D]]		[[Category: Levy, D]]
	[[Category: Iljina, M]]		[[Category: Iljina, M]]
-	[[Category: Dym, O]]
	[[Category: Scheerer, D]]		[[Category: Scheerer, D]]
-	[[Category: ~~Shakhnovich~~, ~~E.I~~]]	+	[[Category: Dym, O]]
	[[Category: Adkar, B.V]]		[[Category: Adkar, B.V]]
		+	[[Category: Shakhnovich, E.I]]

OCA: Protected "8bqf" [edit=sysop:move=sysop]

2022-11-30T08:24:15Z

Protected "8bqf" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:24, 30 November 2022

OCA: New page: '''Unreleased structure''' The entry 8bqf is ON HOLD Authors: Scheerer, D., Adkar, B.V., Bhattacharyya, S., Levy, D., Iljina, M., Iljina, I., Dym, O., Haran, G., Shakhnovich, E.I. Desc...

2022-11-30T08:24:12Z

New page: '''Unreleased structure''' The entry 8bqf is ON HOLD Authors: Scheerer, D., Adkar, B.V., Bhattacharyya, S., Levy, D., Iljina, M., Iljina, I., Dym, O., Haran, G., Shakhnovich, E.I. Desc...

New page

'''Unreleased structure'''

The entry 8bqf is ON HOLD

Authors: Scheerer, D., Adkar, B.V., Bhattacharyya, S., Levy, D., Iljina, M., Iljina, I., Dym, O., Haran, G., Shakhnovich, E.I.

Description: Adenylate Kinase L107I MUTANT
[[Category: Unreleased Structures]]
[[Category: Bhattacharyya, S]]
[[Category: Iljina, I]]
[[Category: Haran, G]]
[[Category: Levy, D]]
[[Category: Iljina, M]]
[[Category: Dym, O]]
[[Category: Scheerer, D]]
[[Category: Shakhnovich, E.I]]
[[Category: Adkar, B.V]]