5dot - Revision history

OCA at 21:53, 28 June 2023

2023-06-28T21:53:16Z

← Older revision		Revision as of 21:53, 28 June 2023
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	<StructureSection load='5dot' size='340' side='right'caption='[[5dot]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5dot' size='340' side='right'caption='[[5dot]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dot]] is a 2 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=5DOT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DOT FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dot]] is a 2 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=5DOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DOT FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.4Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CPS1 ([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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Carbamoyl-phosphate_synthase_~~(~~ammonia~~) ~~Carbamoyl-phosphate synthase (ammonia)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.16 6.3.4.16]~~ </~~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=5dot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dot OCA], [https://pdbe.org/5dot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dot RCSB], [https://www.ebi.ac.uk/pdbsum/5dot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dot 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=5dot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dot OCA], [~~http~~://pdbe.org/5dot PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dot RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dot PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dot ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[~~[http~~://www.uniprot.org/uniprot/CPSM_HUMAN CPSM_HUMAN]] Defects in CPS1 are the cause of carbamoyl phosphate synthetase 1 deficiency (CPS1D) [MIM:[~~http~~://omim.org/entry/237300 237300]]. CPS1D is an autosomal recessive disorder of the urea cycle causing hyperammonemia. Clinical features include protein intolerance, intermittent ataxia, seizures, lethargy, developmental delay and mental retardation.<ref>PMID:9711878</ref> <ref>PMID:12955727</ref> <ref>PMID:12655559</ref> <ref>PMID:11388595</ref> <ref>PMID:11474210</ref> <ref>PMID:15617192</ref> <ref>PMID:15164414</ref> <ref>PMID:16737834</ref> <ref>PMID:17310273</ref> <ref>PMID:20578160</ref> <ref>PMID:20520828</ref> <ref>PMID:21120950</ref> Note=Genetic variations in CPS1 influence the availability of precursors for nitric oxide (NO) synthesis and play a role in clinical situations where endogenous NO production is critically important, such as neonatal pulmonary hypertension, increased pulmonary artery pressure following surgical repair of congenital heart defects or hepatovenocclusive disease following bone marrow transplantation. Infants with neonatal pulmonary hypertension homozygous for Thr-1406 have lower L-arginine concentrations than neonates homozygous for Asn-1406.<ref>PMID:20520828</ref>		[https://www.uniprot.org/uniprot/CPSM_HUMAN CPSM_HUMAN] Defects in CPS1 are the cause of carbamoyl phosphate synthetase 1 deficiency (CPS1D) [MIM:[https://omim.org/entry/237300 237300]. CPS1D is an autosomal recessive disorder of the urea cycle causing hyperammonemia. Clinical features include protein intolerance, intermittent ataxia, seizures, lethargy, developmental delay and mental retardation.<ref>PMID:9711878</ref> <ref>PMID:12955727</ref> <ref>PMID:12655559</ref> <ref>PMID:11388595</ref> <ref>PMID:11474210</ref> <ref>PMID:15617192</ref> <ref>PMID:15164414</ref> <ref>PMID:16737834</ref> <ref>PMID:17310273</ref> <ref>PMID:20578160</ref> <ref>PMID:20520828</ref> <ref>PMID:21120950</ref> Note=Genetic variations in CPS1 influence the availability of precursors for nitric oxide (NO) synthesis and play a role in clinical situations where endogenous NO production is critically important, such as neonatal pulmonary hypertension, increased pulmonary artery pressure following surgical repair of congenital heart defects or hepatovenocclusive disease following bone marrow transplantation. Infants with neonatal pulmonary hypertension homozygous for Thr-1406 have lower L-arginine concentrations than neonates homozygous for Asn-1406.<ref>PMID:20520828</ref>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/CPSM_HUMAN CPSM_HUMAN]] Involved in the urea cycle of ureotelic animals where the enzyme plays an important role in removing excess ammonia from the cell.		[https://www.uniprot.org/uniprot/CPSM_HUMAN CPSM_HUMAN] Involved in the urea cycle of ureotelic animals where the enzyme plays an important role in removing excess ammonia from the cell.
	<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: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Cima, S de]]~~		[[Category: Fita I]]
	[[Category: Fita, I]]		[[Category: Polo LM]]
	[[Category: Polo~~, L M~~]]		[[Category: Rubio V]]
	[[Category: Rubio, V]]		[[Category: De Cima S]]
	[[Category: ~~Adenosine triphosphate]]~~
	~~[[Category: Allosteric site]]~~
	~~[[Category: Ammonia]]~~
	~~[[Category: Apo]]~~
	~~[[Category: Carbamoyl phosphate]]~~
	~~[[Category: Cps1 deficiency]]~~
	~~[[Category: Hyperammonemia]]~~
	~~[[Category: Ligase]]~~
	~~[[Category: Multi-domain]]~~
	~~[[Category: N-acetyl-l-glutamate]]~~
	~~[[Category: Rare disease]]~~
	~~[[Category: Urea cycle~~]]

OCA at 08:12, 8 April 2020

2020-04-08T08:12:56Z

← Older revision		Revision as of 08:12, 8 April 2020
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	==Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form==		==Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form==
	<StructureSection load='5dot' size='340' side='right' caption='[[5dot]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5dot' size='340' side='right'caption='[[5dot]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dot]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DOT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=5DOT FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dot]] is a 2 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=5DOT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DOT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPS1 ([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/Carbamoyl-phosphate_synthase_(ammonia) Carbamoyl-phosphate synthase (ammonia)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.16 6.3.4.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbamoyl-phosphate_synthase_(ammonia) Carbamoyl-phosphate synthase (ammonia)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.16 6.3.4.16] </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=5dot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dot OCA], [http://pdbe.org/5dot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dot RCSB], [http://www.ebi.ac.uk/pdbsum/5dot PDBsum]</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=5dot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dot OCA], [http://pdbe.org/5dot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dot RCSB], [http://www.ebi.ac.uk/pdbsum/5dot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dot ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	</div>		</div>
	<div class="pdbe-citations 5dot" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dot" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Carbamoyl phosphate synthetase 3D structures\|Carbamoyl phosphate synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Cima, S de]]		[[Category: Cima, S de]]
	[[Category: Fita, I]]		[[Category: Fita, I]]

OCA at 13:39, 9 December 2015

2015-12-09T13:39:09Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+==Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form==
-The entry 5dot is ON HOLD  until Paper Publication
+Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.,de Cima S, Polo LM, Diez-Fernandez C, Martinez AI, Cervera J, Fita I, Rubio V Sci Rep. 2015 Nov 23;5:16950. doi: 10.1038/srep16950. PMID:26592762<ref>PMID:26592762</ref>
-Authors: Polo, L.M., de Cima, S., Fita, I., Rubio, V.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form
+<div class="pdbe-citations 5dot" style="background-color:#fffaf0;"></div>
-[[Category: Unreleased Structures]]
+== References ==
 [[Category: Rubio, V]]
-[[Category: Polo, L.M]]
+[[Category: Adenosine triphosphate]]
-[[Category: Fita, I]]
+[[Category: Allosteric site]]
-[[Category: De Cima, S]]
+[[Category: Ammonia]]

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

2015-09-30T13:18:08Z

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

← Older revision	Revision as of 13:18, 30 September 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5dot is ON HOLD until Paper Publication Authors: Polo, L.M., de Cima, S., Fita, I., Rubio, V. Description: Crystal Structure of Human Carbamoyl pho...

2015-09-30T13:18:06Z

New page: '''Unreleased structure''' The entry 5dot is ON HOLD until Paper Publication Authors: Polo, L.M., de Cima, S., Fita, I., Rubio, V. Description: Crystal Structure of Human Carbamoyl pho...

New page

'''Unreleased structure'''

The entry 5dot is ON HOLD until Paper Publication

Authors: Polo, L.M., de Cima, S., Fita, I., Rubio, V.

Description: Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form
[[Category: Unreleased Structures]]
[[Category: Rubio, V]]
[[Category: Polo, L.M]]
[[Category: Fita, I]]
[[Category: De Cima, S]]