7jdw - Revision history

OCA at 10:57, 15 November 2023

OCA — Wed, 15 Nov 2023 10:57:07 GMT

←Older revision		Revision as of 10:57, 15 November 2023
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		+
	==CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID==		==CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID==
-	<StructureSection load='7jdw' size='340' side='right' caption='[[7jdw]], [[Resolution\|resolution]] 2.37Å' scene=''>	+	<StructureSection load='7jdw' size='340' side='right'caption='[[7jdw]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jdw]] is a 1 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=7JDW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=7JDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jdw]] is a 1 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=7JDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JDW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=DAV:DELTA-AMINO+VALERIC+ACID'>DAV</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]] 2.37Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">AT38H ([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=DAV:DELTA-AMINO+VALERIC+ACID'>DAV</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1]~~ </~~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=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jdw OCA], [https://pdbe.org/7jdw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jdw RCSB], [https://www.ebi.ac.uk/pdbsum/7jdw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jdw 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=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jdw OCA], [~~http~~://pdbe.org/7jdw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jdw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jdw PDBsum]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:[~~http~~://omim.org/entry/612718 612718]]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.	+	[https://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN] Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:[https://omim.org/entry/612718 612718]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.<ref>PMID:16820567</ref> <ref>PMID:16125225</ref> <ref>PMID:16614068</ref>	+	[https://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN] Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.<ref>PMID:16820567</ref> <ref>PMID:16125225</ref> <ref>PMID:16614068</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/7jdw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/7jdw_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Glycine amidinotransferase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Fritsche, E]]	+	[[Category: Fritsche E]]
-	[[Category: Huber, R]]	+	[[Category: Huber R]]
-	[[Category: Humm, A]]	+	[[Category: Humm A]]
-	~~[[Category: Catalytic triad]]~~	+
-	~~[[Category: Creatine biosynthesis]]~~	+
-	~~[[Category: Fivefold pseudosymmetry]]~~	+
-	~~[[Category: Novel fold]]~~	+
-	~~[[Category: Reaction mechanism]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 18:19, 9 February 2016

OCA — Tue, 09 Feb 2016 18:19:14 GMT

←Older revision		Revision as of 18:19, 9 February 2016
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	<StructureSection load='7jdw' size='340' side='right' caption='[[7jdw]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='7jdw' size='340' side='right' caption='[[7jdw]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7JDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jdw]] is a 1 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=7JDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7JDW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAV:DELTA-AMINO+VALERIC+ACID'>DAV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAV:DELTA-AMINO+VALERIC+ACID'>DAV</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT38H ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT38H ([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/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1] </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=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7jdw RCSB], [http://www.ebi.ac.uk/pdbsum/7jdw 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=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jdw OCA], [http://pdbe.org/7jdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jdw RCSB], [http://www.ebi.ac.uk/pdbsum/7jdw PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=7jdw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	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 7jdw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Glycine amidinotransferase]]		[[Category: Glycine amidinotransferase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Fritsche, E]]		[[Category: Fritsche, E]]
	[[Category: Huber, R]]		[[Category: Huber, R]]

OCA at 15:09, 21 December 2014

OCA — Sun, 21 Dec 2014 15:09:15 GMT

←Older revision		Revision as of 15:09, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_7jdw\| PDB=7jdw \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID==
-	===CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID===	+	<StructureSection load='7jdw' size='340' side='right' caption='[[7jdw]], [[Resolution\|resolution]] 2.37Å' scene=''>
-	~~{{ABSTRACT_PUBMED_9915841}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[7jdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7JDW FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAV:DELTA-AMINO+VALERIC+ACID'>DAV</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT38H ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1] </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=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7jdw RCSB], [http://www.ebi.ac.uk/pdbsum/7jdw PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:[http://omim.org/entry/612718 612718]]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.		[[http://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:[http://omim.org/entry/612718 612718]]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.<ref>PMID:16820567</ref> <ref>PMID:16125225</ref> <ref>PMID:16614068</ref>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/7jdw_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human L-arginine:glycine amidinotransferase (AT) shows large structural changes of the 300-flap and of helix H9 upon binding of L-arginine and L-ornithine, described as a closed and an open conformation (Humm, A., Fritsche, E., Steinbacher, S., and Huber, R. (1997) EMBO J. 16, 3373-3385). To elucidate the structural basis of these induced-fit movements, the x-ray structures of AT in complex with the amidino acceptor glycine and its analogs gamma-aminobutyric acid and delta-aminovaleric acid, as well as in complex with the amidino donor analogs L-alanine, L-alpha-aminobutyric acid, and L-norvaline, have been solved at 2.6-, 2.5-, 2.37-, 2.3-, 2.5-, and 2.4-A resolutions, respectively. The latter three compounds were found to stabilize the open conformer. The glycine analogs bind in a distinct manner and do not induce the transition to the open state. The complex with glycine revealed a third binding mode, reflecting the rather broad substrate specificity of AT. These findings identified a role for the alpha-amino group of the ligand in stabilizing the open conformer. The kinetic, structural, and thermodynamic properties of the mutants ATDeltaM302 and ATDelta11 (lacks 11 residues of H9) confirmed the key role of Asn300 and suggest that in mammalian amidinotransferases, the role of helix H9 is in accelerating amidino transfer by an induced-fit mechanism. Helix H9 does not add to the stability of the protein.

-	~~==Function==~~	+	The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study.,Fritsche E, Humm A, Huber R J Biol Chem. 1999 Jan 29;274(5):3026-32. PMID:9915841<ref>PMID:9915841</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/GATM_HUMAN GATM_HUMAN]] Catalyzes the biosynthesis of guanidinoacetate~~, ~~the immediate precursor of creatine~~. ~~Creatine plays a vital role in energy metabolism in muscle tissues~~. ~~May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.<ref>~~PMID:~~16820567</ref>~~<ref>PMID:~~16125225~~</ref>~~<ref>PMID:16614068</ref>~~	+
-		+
-	~~==About this Structure==~~	+
-	[[7jdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:009915841</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Glycine amidinotransferase]]		[[Category: Glycine amidinotransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Fritsche, E.]]	+	[[Category: Fritsche, E]]
-	[[Category: Huber, R.]]	+	[[Category: Huber, R]]
-	[[Category: Humm, A.]]	+	[[Category: Humm, A]]
	[[Category: Catalytic triad]]		[[Category: Catalytic triad]]
	[[Category: Creatine biosynthesis]]		[[Category: Creatine biosynthesis]]

OCA: Protected "7jdw" [edit=sysop:move=sysop]

OCA — Sun, 24 Mar 2013 17:04:28 GMT

Protected "7jdw" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:04, 24 March 2013

OCA at 17:04, 24 March 2013

OCA — Sun, 24 Mar 2013 17:04:27 GMT

←Older revision		Revision as of 17:04, 24 March 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:7jdw.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_7jdw", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_7jdw\| PDB=7jdw \| SCENE= }}		{{STRUCTURE_7jdw\| PDB=7jdw \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID===		===CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID===
		+	{{ABSTRACT_PUBMED_9915841}}

		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:[http://omim.org/entry/612718 612718]]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.

-	~~<!--~~	+	==Function==
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_9915841}}, adds the Publication Abstract to the page~~	+	[[http://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN]] Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.<ref>PMID:16820567</ref><ref>PMID:16125225</ref><ref>PMID:16614068</ref>
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov)~~, ~~where 9915841 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_9915841}}~~	+

	==About this Structure==		==About this Structure==
-	~~7JDW~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].	+	[[7jdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9915841~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009915841</ref><references group="xtra"/><references/>
	[[Category: Glycine amidinotransferase]]		[[Category: Glycine amidinotransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 34:		Line 24:
	[[Category: Novel fold]]		[[Category: Novel fold]]
	[[Category: Reaction mechanism]]		[[Category: Reaction mechanism]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 11:45:51 2009''~~	+

OCA at 09:45, 17 February 2009

OCA — Tue, 17 Feb 2009 09:45:51 GMT

←Older revision		Revision as of 09:45, 17 February 2009
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	==About this Structure==		==About this Structure==
-	7JDW is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].	+	7JDW is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].

	==Reference==		==Reference==
-	~~The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study., Fritsche E, Humm A, Huber R, J Biol Chem. 1999 Jan 29;274(5):3026-32.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9915841 9915841]~~	+	<ref group="xtra">PMID:9915841</ref><references group="xtra"/>
	[[Category: Glycine amidinotransferase]]		[[Category: Glycine amidinotransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Fritsche, E.]]		[[Category: Fritsche, E.]]
	[[Category: Huber, R.]]		[[Category: Huber, R.]]
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	[[Category: Reaction mechanism]]		[[Category: Reaction mechanism]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:40:~~36 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:45:51 2009''

OCA at 11:40, 3 July 2008

OCA — Thu, 03 Jul 2008 11:40:37 GMT

←Older revision		Revision as of 11:40, 3 July 2008
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-	[[Image:7jdw.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:7jdw.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_7jdw\| PDB=7jdw \| SCENE= }}		{{STRUCTURE_7jdw\| PDB=7jdw \| SCENE= }}

-	~~'''~~CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID~~'''~~	+	===CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID===


-	~~==Overview==~~	+	<!--
-	~~Human L~~-~~arginine:glycine amidinotransferase (AT) shows large structural changes of the 300~~-~~flap and of helix H9 upon binding of L-arginine and L-ornithine~~, ~~described as a closed and an open conformation (Humm~~, ~~A., Fritsche, E., Steinbacher, S., and Huber, R. (1997) EMBO J. 16, 3373-3385). To elucidate~~ the ~~structural basis of these induced-fit movements,~~ the ~~x-ray structures of AT in complex with the amidino acceptor glycine and its analogs gamma-aminobutyric acid and delta-aminovaleric acid,~~ as ~~well as in complex with the amidino donor analogs L-alanine, L-alpha-aminobutyric acid, and L-norvaline, have been solved~~ at 2.~~6-, 2~~.5-, ~~2.37-, 2.3-, 2.5-, and 2.4-A resolutions, respectively. The latter three compounds were found to stabilize~~ the ~~open conformer~~. The glycine analogs bind in a distinct manner and do not induce the transition to the open state. The complex with glycine revealed a third binding mode, reflecting the rather broad substrate specificity of AT. These findings identified a role for the alpha-amino group of the ligand in stabilizing the open conformer. The kinetic, structural, and thermodynamic properties of the mutants ATDeltaM302 and ATDelta11 (lacks 11 residues of H9) confirmed the key role of Asn300 and suggest that in mammalian amidinotransferases, the role of helix H9 is in accelerating amidino transfer by an induced-~~fit mechanism. Helix H9 does not add to the stability of the protein.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9915841}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9915841 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9915841}}

	==About this Structure==		==About this Structure==
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	[[Category: Novel fold]]		[[Category: Novel fold]]
	[[Category: Reaction mechanism]]		[[Category: Reaction mechanism]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:46:26 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:40:36 2008''

OCA at 19:46, 4 May 2008

OCA — Sun, 04 May 2008 19:46:26 GMT

←Older revision		Revision as of 19:46, 4 May 2008
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	[[Image:7jdw.jpg\|left\|200px]]		[[Image:7jdw.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 7jdw \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>7jdw</scene>, resolution 2.37Å~~	+	The line below this paragraph, containing "STRUCTURE_7jdw", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DAV:DELTA~~-~~AMINO+VALERIC+ACID'>DAV</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase]~~, ~~with EC number [http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1] </span>~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= AT38H~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]~~)	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_7jdw\| PDB=7jdw \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	~~\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca~~-~~docs/fgij/fg.htm?mol=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca~~-~~bin/ocaids?id~~=7jdw ~~OCA], [http://www.ebi.ac.uk/pdbsum/7jdw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId~~=~~7jdw RCSB]</span>~~	+
-	}}	+

	'''CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID'''		'''CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID'''
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	[[Category: Huber, R.]]		[[Category: Huber, R.]]
	[[Category: Humm, A.]]		[[Category: Humm, A.]]
-	[[Category: ~~catalytic~~ triad]]	+	[[Category: Catalytic triad]]
-	[[Category: ~~creatine~~ biosynthesis]]	+	[[Category: Creatine biosynthesis]]
-	[[Category: ~~fivefold~~ pseudosymmetry]]	+	[[Category: Fivefold pseudosymmetry]]
-	[[Category: ~~novel~~ fold]]	+	[[Category: Novel fold]]
-	[[Category: ~~reaction~~ mechanism]]	+	[[Category: Reaction mechanism]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:46:26 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:44:28 2008''	+

OCA at 02:44, 31 March 2008

OCA — Mon, 31 Mar 2008 02:44:33 GMT

←Older revision		Revision as of 02:44, 31 March 2008
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	\|PDB= 7jdw \|SIZE=350\|CAPTION= <scene name='initialview01'>7jdw</scene>, resolution 2.37Å		\|PDB= 7jdw \|SIZE=350\|CAPTION= <scene name='initialview01'>7jdw</scene>, resolution 2.37Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=DAV:DELTA-AMINO VALERIC ACID'>DAV</scene>	+	\|LIGAND= <scene name='pdbligand=DAV:DELTA-AMINO+VALERIC+ACID'>DAV</scene>
-	\|ACTIVITY= [http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1]	+	\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1] </span>
	\|GENE= AT38H ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])		\|GENE= AT38H ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7jdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jdw OCA], [http://www.ebi.ac.uk/pdbsum/7jdw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7jdw RCSB]</span>
	}}		}}

Line 14:		Line 17:
	==Overview==		==Overview==
	Human L-arginine:glycine amidinotransferase (AT) shows large structural changes of the 300-flap and of helix H9 upon binding of L-arginine and L-ornithine, described as a closed and an open conformation (Humm, A., Fritsche, E., Steinbacher, S., and Huber, R. (1997) EMBO J. 16, 3373-3385). To elucidate the structural basis of these induced-fit movements, the x-ray structures of AT in complex with the amidino acceptor glycine and its analogs gamma-aminobutyric acid and delta-aminovaleric acid, as well as in complex with the amidino donor analogs L-alanine, L-alpha-aminobutyric acid, and L-norvaline, have been solved at 2.6-, 2.5-, 2.37-, 2.3-, 2.5-, and 2.4-A resolutions, respectively. The latter three compounds were found to stabilize the open conformer. The glycine analogs bind in a distinct manner and do not induce the transition to the open state. The complex with glycine revealed a third binding mode, reflecting the rather broad substrate specificity of AT. These findings identified a role for the alpha-amino group of the ligand in stabilizing the open conformer. The kinetic, structural, and thermodynamic properties of the mutants ATDeltaM302 and ATDelta11 (lacks 11 residues of H9) confirmed the key role of Asn300 and suggest that in mammalian amidinotransferases, the role of helix H9 is in accelerating amidino transfer by an induced-fit mechanism. Helix H9 does not add to the stability of the protein.		Human L-arginine:glycine amidinotransferase (AT) shows large structural changes of the 300-flap and of helix H9 upon binding of L-arginine and L-ornithine, described as a closed and an open conformation (Humm, A., Fritsche, E., Steinbacher, S., and Huber, R. (1997) EMBO J. 16, 3373-3385). To elucidate the structural basis of these induced-fit movements, the x-ray structures of AT in complex with the amidino acceptor glycine and its analogs gamma-aminobutyric acid and delta-aminovaleric acid, as well as in complex with the amidino donor analogs L-alanine, L-alpha-aminobutyric acid, and L-norvaline, have been solved at 2.6-, 2.5-, 2.37-, 2.3-, 2.5-, and 2.4-A resolutions, respectively. The latter three compounds were found to stabilize the open conformer. The glycine analogs bind in a distinct manner and do not induce the transition to the open state. The complex with glycine revealed a third binding mode, reflecting the rather broad substrate specificity of AT. These findings identified a role for the alpha-amino group of the ligand in stabilizing the open conformer. The kinetic, structural, and thermodynamic properties of the mutants ATDeltaM302 and ATDelta11 (lacks 11 residues of H9) confirmed the key role of Asn300 and suggest that in mammalian amidinotransferases, the role of helix H9 is in accelerating amidino transfer by an induced-fit mechanism. Helix H9 does not add to the stability of the protein.
-
-	==Disease==
-	Known diseases associated with this structure: AGAT deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602360 602360]]

	==About this Structure==		==About this Structure==
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	[[Category: Huber, R.]]		[[Category: Huber, R.]]
	[[Category: Humm, A.]]		[[Category: Humm, A.]]
-	[[Category: DAV]]
	[[Category: catalytic triad]]		[[Category: catalytic triad]]
	[[Category: creatine biosynthesis]]		[[Category: creatine biosynthesis]]
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	[[Category: reaction mechanism]]		[[Category: reaction mechanism]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:14:47 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:44:28 2008''

OCA at 17:14, 20 March 2008

OCA — Thu, 20 Mar 2008 17:14:49 GMT

←Older revision		Revision as of 17:14, 20 March 2008
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-	[[Image:7jdw.jpg\|left\|200px]]~~<br /><applet load~~="7jdw~~" size~~="350~~" color~~=~~"white" frame="true" align="right" spinBox="true"~~	+	[[Image:7jdw.jpg\|left\|200px]]
-	~~caption~~="7jdw, resolution 2.37Å" />	+
-	'''CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID'''~~<br />~~	+	{{Structure
		+	\|PDB= 7jdw \|SIZE=350\|CAPTION= <scene name='initialview01'>7jdw</scene>, resolution 2.37Å
		+	\|SITE=
		+	\|LIGAND= <scene name='pdbligand=DAV:DELTA-AMINO VALERIC ACID'>DAV</scene>
		+	\|ACTIVITY= [http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1]
		+	\|GENE= AT38H ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
		+	}}
		+
		+	'''CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID'''
		+

	==Overview==		==Overview==
Line 10:		Line 19:

	==About this Structure==		==About this Structure==
-	7JDW is a [~~http://en.wikipedia.org/wiki/Single_protein~~ Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] ~~with <scene name='pdbligand=DAV:'>DAV</scene> as [http://en~~.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycine_amidinotransferase Glycine amidinotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.4.1 2.1.4.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].	+	7JDW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JDW OCA].

	==Reference==		==Reference==
-	The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study., Fritsche E, Humm A, Huber R, J Biol Chem. 1999 Jan 29;274(5):3026-32. PMID:[http://~~ispc~~.~~weizmann~~.ac.~~il/~~/~~pmbin~~/~~getpm?pmid=~~9915841 9915841]	+	The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study., Fritsche E, Humm A, Huber R, J Biol Chem. 1999 Jan 29;274(5):3026-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9915841 9915841]
	[[Category: Glycine amidinotransferase]]		[[Category: Glycine amidinotransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
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	[[Category: reaction mechanism]]		[[Category: reaction mechanism]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Feb 21~~ 19:17:24 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:14:47 2008''