5u92 - Revision history

OCA at 13:23, 4 October 2023

OCA — Wed, 04 Oct 2023 13:23:23 GMT

←Older revision		Revision as of 13:23, 4 October 2023
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	<StructureSection load='5u92' size='340' side='right'caption='[[5u92]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5u92' size='340' side='right'caption='[[5u92]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u92]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Polybetes_pythagoricus Polybetes pythagoricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U92 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u92]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Polybetes_pythagoricus Polybetes pythagoricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U92 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ARG:ARGININE'>ARG</scene~~>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CSO~~:~~S-HYDROXYCYSTEINE~~'>~~CSO~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[5u8e\|5u8e]]</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=5u92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u92 OCA], [https://pdbe.org/5u92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u92 RCSB], [https://www.ebi.ac.uk/pdbsum/5u92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u92 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Arginine_kinase Arginine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.3.3 2.7.3.3]~~ </~~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=5u92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u92 OCA], [~~http~~://pdbe.org/5u92 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u92 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u92 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u92 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KARG_POLPT KARG_POLPT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arginine kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Polybetes pythagoricus]]		[[Category: Polybetes pythagoricus]]
-	[[Category: Garcia~~, C F~~]]	+	[[Category: Garcia CF]]
-	[[Category: Lopez-zavala~~, A A~~]]	+	[[Category: Lopez-zavala AA]]
-	[[Category: Paredes-Hernandez, J]]	+	[[Category: Paredes-Hernandez J]]
-	[[Category: Sotelo-Mundo~~, R R~~]]	+	[[Category: Sotelo-Mundo RR]]
-	[[Category: Stojanoff, V]]	+	[[Category: Stojanoff V]]
-	~~[[Category: Binary complex]]~~	+
-	~~[[Category: Phosphagen metabolism]]~~	+
-	~~[[Category: Spider]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:28, 4 December 2019

OCA — Wed, 04 Dec 2019 09:28:40 GMT

←Older revision		Revision as of 09:28, 4 December 2019
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	==Crystal Structure of arginine kinase from the spider Polybetes pythagoricus in complex with arginine==		==Crystal Structure of arginine kinase from the spider Polybetes pythagoricus in complex with arginine==
-	<StructureSection load='5u92' size='340' side='right' caption='[[5u92]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5u92' size='340' side='right'caption='[[5u92]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u92]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u92]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Polybetes_pythagoricus Polybetes pythagoricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U92 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5u92" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5u92" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Arginine kinase 3D structures\|Arginine kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Arginine kinase]]		[[Category: Arginine kinase]]
		+	[[Category: Large Structures]]
		+	[[Category: Polybetes pythagoricus]]
	[[Category: Garcia, C F]]		[[Category: Garcia, C F]]
	[[Category: Lopez-zavala, A A]]		[[Category: Lopez-zavala, A A]]
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	[[Category: Binary complex]]		[[Category: Binary complex]]
	[[Category: Phosphagen metabolism]]		[[Category: Phosphagen metabolism]]
-	[[Category: Polybetes pythagoricus]]
	[[Category: Spider]]		[[Category: Spider]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:28, 4 October 2017

OCA — Wed, 04 Oct 2017 09:28:26 GMT

←Older revision		Revision as of 09:28, 4 October 2017
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	<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=5u92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u92 OCA], [http://pdbe.org/5u92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u92 RCSB], [http://www.ebi.ac.uk/pdbsum/5u92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u92 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=5u92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u92 OCA], [http://pdbe.org/5u92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u92 RCSB], [http://www.ebi.ac.uk/pdbsum/5u92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u92 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km ) was 1.7 mM with a kcat of 75 s-1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310-320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.
		+
		+	Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus.,Laino A, Lopez-Zavala AA, Garcia-Orozco KD, Carrasco-Miranda JS, Santana M, Stojanoff V, Sotelo-Mundo RR, Garcia CF PeerJ. 2017 Sep 11;5:e3787. doi: 10.7717/peerj.3787. eCollection 2017. PMID:28924503<ref>PMID:28924503</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5u92" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:33, 13 September 2017

OCA — Wed, 13 Sep 2017 09:33:48 GMT

←Older revision		Revision as of 09:33, 13 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u92 ~~is ON HOLD~~	+	==Crystal Structure of arginine kinase from the spider Polybetes pythagoricus in complex with arginine==
-		+	<StructureSection load='5u92' size='340' side='right' caption='[[5u92]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Lopez~~-~~zavala~~, A.A., ~~Garcia, C~~.F, ~~Paredes~~-~~Hernandez~~, J., ~~Stojanoff~~, V., ~~Sotelo~~-~~Mundo, R.R~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5u92]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U92 FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of arginine~~ kinase ~~from the spider Polybetes pythagoricus in complex with arginine~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8e\|5u8e]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_kinase Arginine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.3.3 2.7.3.3] </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=5u92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u92 OCA], [http://pdbe.org/5u92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u92 RCSB], [http://www.ebi.ac.uk/pdbsum/5u92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u92 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arginine kinase]]
		+	[[Category: Garcia, C F]]
		+	[[Category: Lopez-zavala, A A]]
		+	[[Category: Paredes-Hernandez, J]]
		+	[[Category: Sotelo-Mundo, R R]]
	[[Category: Stojanoff, V]]		[[Category: Stojanoff, V]]
-	[[Category: ~~Lopez-Zavala, A.A~~]]	+	[[Category: Binary complex]]
-	[[Category: ~~Sotelo-Mundo, R.R~~]]	+	[[Category: Phosphagen metabolism]]
-	[[Category: ~~Garcia, C.F, Paredes-Hernandez, J~~]]	+	[[Category: Polybetes pythagoricus]]
		+	[[Category: Spider]]
		+	[[Category: Transferase]]

OCA: Protected "5u92" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:34:03 GMT

Protected "5u92" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:34, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u92 is ON HOLD Authors: Lopez-zavala, A.A., Garcia, C.F, Paredes-Hernandez, J., Stojanoff, V., Sotelo-Mundo, R.R. Description: Crystal Structure o...

OCA — Thu, 22 Dec 2016 20:34:01 GMT

New page: '''Unreleased structure''' The entry 5u92 is ON HOLD Authors: Lopez-zavala, A.A., Garcia, C.F, Paredes-Hernandez, J., Stojanoff, V., Sotelo-Mundo, R.R. Description: Crystal Structure o...

New page

'''Unreleased structure'''

The entry 5u92 is ON HOLD

Authors: Lopez-zavala, A.A., Garcia, C.F, Paredes-Hernandez, J., Stojanoff, V., Sotelo-Mundo, R.R.

Description: Crystal Structure of arginine kinase from the spider Polybetes pythagoricus in complex with arginine
[[Category: Unreleased Structures]]
[[Category: Stojanoff, V]]
[[Category: Lopez-Zavala, A.A]]
[[Category: Sotelo-Mundo, R.R]]
[[Category: Garcia, C.F, Paredes-Hernandez, J]]