6zjb - Revision history

OCA at 11:53, 1 February 2024

OCA — Thu, 01 Feb 2024 11:53:23 GMT

←Older revision		Revision as of 11:53, 1 February 2024
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	<StructureSection load='6zjb' size='340' side='right'caption='[[6zjb]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='6zjb' size='340' side='right'caption='[[6zjb]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zjb]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZJB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zjb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZJB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=G5P:P1~~-~~(5-ADENOSYL)-P5-(5-GUANOSYL)+PENTAPHOSPHATE'>G5P</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.822Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AK3, AK3L1, AK6, AKL3L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G5P:P1-(5-ADENOSYL)-P5-(5-GUANOSYL)+PENTAPHOSPHATE'>G5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate--adenylate_kinase Nucleoside-triphosphate--adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.10 2.7.4.10] </~~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=6zjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjb OCA], [https://pdbe.org/6zjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zjb RCSB], [https://www.ebi.ac.uk/pdbsum/6zjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjb ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6zjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjb OCA], [~~http~~://pdbe.org/6zjb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zjb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zjb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjb ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KAD3_HUMAN KAD3_HUMAN]
	<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 6zjb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6zjb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nucleoside-triphosphate--adenylate kinase]]~~	+	[[Category: Grundstrom C]]
-	[[Category: Grundstrom, C]]	+	[[Category: Rogne P]]
-	[[Category: Rogne, P]]	+	[[Category: Sauer-Eriksson AE]]
-	[[Category: Sauer-Eriksson~~, A E~~]]	+	[[Category: Wolf-Watz M]]
-	[[Category: Wolf-Watz, M]]	+
-	~~[[Category: Gp5a]]~~	+
-	~~[[Category: Gtp:amp phosphotransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:42, 7 October 2020

OCA — Wed, 07 Oct 2020 06:42:19 GMT

←Older revision		Revision as of 06:42, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A==		==Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A==
-	<StructureSection load='6zjb' size='340' side='right'caption='[[6zjb]]' scene=''>	+	<StructureSection load='6zjb' size='340' side='right'caption='[[6zjb]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZJB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zjb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZJB FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjb OCA], [http://pdbe.org/6zjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zjb RCSB], [http://www.ebi.ac.uk/pdbsum/6zjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjb ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G5P:P1-(5-ADENOSYL)-P5-(5-GUANOSYL)+PENTAPHOSPHATE'>G5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AK3, AK3L1, AK6, AKL3L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate--adenylate_kinase Nucleoside-triphosphate--adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.10 2.7.4.10] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjb OCA], [http://pdbe.org/6zjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zjb RCSB], [http://www.ebi.ac.uk/pdbsum/6zjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjb ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ATP and GTP are exceptionally important molecules in biology with multiple, and often discrete, functions. Therefore, enzymes that bind to either of them must develop robust mechanisms to selectively utilize one or the other. Here, this specific problem is addressed by molecular studies of the human NMP kinase AK3, which uses GTP to phosphorylate AMP. AK3 plays an important role in the citric acid cycle, where it is responsible for GTP/GDP recycling. By combining a structural biology approach with functional experiments, we present a comprehensive structural and mechanistic understanding of the enzyme. We discovered that AK3 functions by recruitment of GTP to the active site, while ATP is rejected and nonproductively bound to the AMP binding site. Consequently, ATP acts as an inhibitor with respect to GTP and AMP. The overall features with specific recognition of the correct substrate and nonproductive binding by the incorrect substrate bear a strong similarity to previous findings for the ATP specific NMP kinase adenylate kinase. Taken together, we are now able to provide the fundamental principles for GTP and ATP selectivity in the large NMP kinase family. As a side-result originating from nonlinearity of chemical shifts in GTP and ATP titrations, we find that protein surfaces offer a general and weak binding affinity for both GTP and ATP. These nonspecific interactions likely act to lower the available intracellular GTP and ATP concentrations and may have driven evolution of the Michaelis constants of NMP kinases accordingly.
		+
		+	Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.,Rogne P, Dulko-Smith B, Goodman J, Rosselin M, Grundstrom C, Hedberg C, Nam K, Sauer-Eriksson AE, Wolf-Watz M Biochemistry. 2020 Sep 11. doi: 10.1021/acs.biochem.0c00549. PMID:32822537<ref>PMID:32822537</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zjb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grundstrom C]]	+	[[Category: Nucleoside-triphosphate--adenylate kinase]]
-	[[Category: Rogne P]]	+	[[Category: Grundstrom, C]]
-	[[Category: Sauer-Eriksson AE]]	+	[[Category: Rogne, P]]
-	[[Category: Wolf-Watz M]]	+	[[Category: Sauer-Eriksson, A E]]
		+	[[Category: Wolf-Watz, M]]
		+	[[Category: Gp5a]]
		+	[[Category: Gtp:amp phosphotransferase]]
		+	[[Category: Transferase]]

OCA at 09:53, 16 September 2020

OCA — Wed, 16 Sep 2020 09:53:34 GMT

←Older revision		Revision as of 09:53, 16 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zjb is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A==
-		+	<StructureSection load='6zjb' size='340' side='right'caption='[[6zjb]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZJB FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjb OCA], [http://pdbe.org/6zjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zjb RCSB], [http://www.ebi.ac.uk/pdbsum/6zjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjb ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Grundstrom C]]
		+	[[Category: Rogne P]]
		+	[[Category: Sauer-Eriksson AE]]
		+	[[Category: Wolf-Watz M]]

OCA at 09:29, 29 July 2020

OCA — Wed, 29 Jul 2020 09:29:36 GMT

←Older revision		Revision as of 09:29, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 08 Jul 2020 11:13:24 GMT

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

←Older revision

Revision as of 11:13, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zjb is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Jul 2020 11:13:23 GMT

New page: '''Unreleased structure''' The entry 6zjb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6zjb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]