4jz7 - Revision history

OCA at 15:51, 20 September 2023

OCA — Wed, 20 Sep 2023 15:51:46 GMT

←Older revision		Revision as of 15:51, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_lamblia_ATCC_50803 Giardia lamblia ATCC 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_lamblia_ATCC_50803 Giardia lamblia ATCC 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</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]] 2.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [https://pdbe.org/4jz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [https://www.ebi.ac.uk/pdbsum/4jz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jz7 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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [https://pdbe.org/4jz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [https://www.ebi.ac.uk/pdbsum/4jz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jz7 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:31, 30 November 2022

OCA — Wed, 30 Nov 2022 11:31:40 GMT

←Older revision		Revision as of 11:31, 30 November 2022
Line 1:		Line 1:

	==Carbamate kinase from Giardia lamblia bound to AMP-PNP==		==Carbamate kinase from Giardia lamblia bound to AMP-PNP==
-	<StructureSection load='4jz7' size='340' side='right' caption='[[4jz7]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='4jz7' size='340' side='right'caption='[[4jz7]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Giaic Giaic~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_lamblia_ATCC_50803 Giardia lamblia ATCC 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kzf\|3kzf]], [[4jz8\|4jz8]], [[4jz9\|4jz9]]</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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [https://pdbe.org/4jz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [https://www.ebi.ac.uk/pdbsum/4jz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jz7 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GL50803_16453 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=184922 GIAIC])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbamate_kinase Carbamate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.2 2.7.2.2] </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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [~~http~~://pdbe.org/4jz7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jz7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jz7 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A8BB85_GIAIC A8BB85_GIAIC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carbamate kinase~~]]	+	[[Category: Giardia lamblia ATCC 50803]]
-	[[Category: ~~Giaic~~]]	+	[[Category: Large Structures]]
-	[[Category: Herzberg, O]]	+	[[Category: Herzberg O]]
-	[[Category: Lim, K]]	+	[[Category: Lim K]]
-	~~[[Category: Adp]]~~	+
-	~~[[Category: Atp carbamate phosphotransferase]]~~	+
-	~~[[Category: Carbamoyl phosphate]]~~	+
-	~~[[Category: Mg2+]]~~	+
-	~~[[Category: Modified rossmann fold]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:53, 4 August 2016

OCA — Thu, 04 Aug 2016 09:53:16 GMT

←Older revision		Revision as of 09:53, 4 August 2016
Line 1:		Line 1:
		+
	==Carbamate kinase from Giardia lamblia bound to AMP-PNP==		==Carbamate kinase from Giardia lamblia bound to AMP-PNP==
	<StructureSection load='4jz7' size='340' side='right' caption='[[4jz7]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='4jz7' size='340' side='right' caption='[[4jz7]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Giardia_lamblia_atcc_50803 Giardia lamblia atcc 50803~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Giaic Giaic]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kzf\|3kzf]], [[4jz8\|4jz8]], [[4jz9\|4jz9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kzf\|3kzf]], [[4jz8\|4jz8]], [[4jz9\|4jz9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GL50803_16453 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=184922 ~~Giardia lamblia ATCC 50803~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GL50803_16453 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=184922 GIAIC])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbamate_kinase Carbamate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.2 2.7.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbamate_kinase Carbamate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.2 2.7.2.2] </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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [http://www.ebi.ac.uk/pdbsum/4jz7 PDBsum]</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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [http://pdbe.org/4jz7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [http://www.ebi.ac.uk/pdbsum/4jz7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jz7 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4jz7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Carbamate kinase]]		[[Category: Carbamate kinase]]
-	[[Category: ~~Giardia lamblia atcc 50803~~]]	+	[[Category: Giaic]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Lim, K]]		[[Category: Lim, K]]

OCA at 14:35, 21 December 2014

OCA — Sun, 21 Dec 2014 14:35:30 GMT

←Older revision		Revision as of 14:35, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4jz7~~\| ~~PDB~~=4jz7 \| ~~SCENE~~= }}	+	==Carbamate kinase from Giardia lamblia bound to AMP-PNP==
-	===Carbamate kinase from Giardia lamblia ~~bound~~ to AMP-PNP~~===~~	+	<StructureSection load='4jz7' size='340' side='right' caption='[[4jz7]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23700444}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jz7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Giardia_lamblia_atcc_50803 Giardia lamblia atcc 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZ7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kzf\|3kzf]], [[4jz8\|4jz8]], [[4jz9\|4jz9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GL50803_16453 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=184922 Giardia lamblia ATCC 50803])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbamate_kinase Carbamate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.2 2.7.2.2] </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=4jz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jz7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jz7 RCSB], [http://www.ebi.ac.uk/pdbsum/4jz7 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK) with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5'-adenylyl-beta,gamma-imidodiphosphate (AMP-PNP), was determined at 2.6 A resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 A resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123-170), which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent.

-	~~==About this Structure==~~	+	Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP.,Lim K, Kulakova L, Galkin A, Herzberg O PLoS One. 2013 May 20;8(5):e64004. doi: 10.1371/journal.pone.0064004. Print 2013. PMID:23700444<ref>PMID:23700444</ref>
-	~~[[4jz7]] is a 4 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Giardia_lamblia_atcc_50803~~ Giardia lamblia ~~atcc 50803]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4JZ7 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023700444</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Carbamate kinase]]		[[Category: Carbamate kinase]]
	[[Category: Giardia lamblia atcc 50803]]		[[Category: Giardia lamblia atcc 50803]]
-	[[Category: Herzberg, O.]]	+	[[Category: Herzberg, O]]
-	[[Category: Lim, K.]]	+	[[Category: Lim, K]]
	[[Category: Adp]]		[[Category: Adp]]
	[[Category: Atp carbamate phosphotransferase]]		[[Category: Atp carbamate phosphotransferase]]

OCA at 13:39, 19 June 2013

OCA — Wed, 19 Jun 2013 13:39:47 GMT

←Older revision		Revision as of 13:39, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4jz7\| PDB=4jz7 \| SCENE= }}
		+	===Carbamate kinase from Giardia lamblia bound to AMP-PNP===
		+	{{ABSTRACT_PUBMED_23700444}}

-	~~The entry~~ 4jz7 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4jz7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Giardia_lamblia_atcc_50803 Giardia lamblia atcc 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JZ7 OCA].

-	~~Authors~~: ~~Lim, K.,~~ Herzberg, O.	+	==Reference==
-		+	<ref group="xtra">PMID:023700444</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Carbamate kinase from Giardia lamblia bound to AMP-PNP~~	+	[[Category: Carbamate kinase]]
		+	[[Category: Giardia lamblia atcc 50803]]
		+	[[Category: Herzberg, O.]]
		+	[[Category: Lim, K.]]
		+	[[Category: Adp]]
		+	[[Category: Atp carbamate phosphotransferase]]
		+	[[Category: Carbamoyl phosphate]]
		+	[[Category: Mg2+]]
		+	[[Category: Modified rossmann fold]]
		+	[[Category: Transferase]]

OCA: Protected "4jz7" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2013 20:03:26 GMT

Protected "4jz7" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:03, 17 April 2013

OCA: New page: '''Unreleased structure''' The entry 4jz7 is ON HOLD until Paper Publication Authors: Lim, K., Herzberg, O. Description: Carbamate kinase from Giardia lamblia bound to AMP-PNP

OCA — Wed, 17 Apr 2013 20:03:25 GMT

New page: '''Unreleased structure''' The entry 4jz7 is ON HOLD until Paper Publication Authors: Lim, K., Herzberg, O. Description: Carbamate kinase from Giardia lamblia bound to AMP-PNP

New page

'''Unreleased structure'''

The entry 4jz7 is ON HOLD until Paper Publication

Authors: Lim, K., Herzberg, O.

Description: Carbamate kinase from Giardia lamblia bound to AMP-PNP