1wsr - Revision history

OCA at 13:34, 13 March 2024

OCA — Wed, 13 Mar 2024 13:34:01 GMT

←Older revision		Revision as of 13:34, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wsr' size='340' side='right'caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1wsr' size='340' side='right'caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wsr]] 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1WSR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wsr]] 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WSR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1wsv\|1wsv]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GCST ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [https://pdbe.org/1wsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [https://www.ebi.ac.uk/pdbsum/1wsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsr 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/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10]~~ </~~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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [~~http~~://pdbe.org/1wsr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wsr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[~~http~~://omim.org/entry/605899 605899]]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref> <ref>PMID:9600239</ref> <ref>PMID:9621520</ref> <ref>PMID:10873393</ref> <ref>PMID:11286506</ref>	+	[https://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[https://omim.org/entry/605899 605899]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref> <ref>PMID:9600239</ref> <ref>PMID:9621520</ref> <ref>PMID:10873393</ref> <ref>PMID:11286506</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] The glycine cleavage system catalyzes the degradation of glycine.	+	[https://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN] The glycine cleavage system catalyzes the degradation of glycine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 22:
	</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=1wsr 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=1wsr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	T-protein, a component of the glycine cleavage system, catalyzes the formation of ammonia and 5,10-methylenetetrahydrofolate from the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein. Several mutations in the human T-protein gene cause non-ketotic hyperglycinemia. To gain insights into the effect of disease-causing mutations and the catalytic mechanism at the molecular level, crystal structures of human T-protein in free form and that bound to 5-methyltetrahydrofolate (5-CH3-H4folate) have been determined at 2.0 A and 2.6 A resolution, respectively. The overall structure consists of three domains arranged in a cloverleaf-like structure with the central cavity, where 5-CH3-H4folate is bound in a kinked shape with the pteridine group deeply buried into the hydrophobic pocket and the glutamyl group pointed to the C-terminal side surface. Most of the disease-related residues cluster around the cavity, forming extensive hydrogen bonding networks. These hydrogen bonding networks are employed in holding not only the folate-binding space but also the positions and the orientations of alpha-helix G and the following loop in the middle region, which seems to play a pivotal role in the T-protein catalysis. Structural and mutational analyses demonstrated that Arg292 interacts through water molecules with the folate polyglutamate tail, and that the invariant Asp101, located close to the N10 group of 5-CH3-H4folate, might play a key role in the initiation of the catalysis by increasing the nucleophilic character of the N10 atom of the folate substrate for the nucleophilic attack on the aminomethyl lipoate intermediate. A clever mechanism of recruiting the aminomethyl lipoate arm to the reaction site seems to function as a way of avoiding the release of toxic formaldehyde.
-
-	Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.,Okamura-Ikeda K, Hosaka H, Yoshimura M, Yamashita E, Toma S, Nakagawa A, Fujiwara K, Motokawa Y, Taniguchi H J Mol Biol. 2005 Sep 2;351(5):1146-59. PMID:16051266<ref>PMID:16051266</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wsr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 40:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aminomethyltransferase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fujiwara, K]]	+	[[Category: Fujiwara K]]
-	[[Category: Hosaka, H]]	+	[[Category: Hosaka H]]
-	[[Category: Motokawa, Y]]	+	[[Category: Motokawa Y]]
-	[[Category: Nakagawa, A]]	+	[[Category: Nakagawa A]]
-	[[Category: Okamura-Ikeda, K]]	+	[[Category: Okamura-Ikeda K]]
-	[[Category: Taniguchi, H]]	+	[[Category: Taniguchi H]]
-	[[Category: Toma, S]]	+	[[Category: Toma S]]
-	[[Category: Yamashita, E]]	+	[[Category: Yamashita E]]
-	[[Category: Yoshimura, M]]	+	[[Category: Yoshimura M]]
-	~~[[Category: Aminomethyl transferase]]~~	+
-	~~[[Category: Glycine-cleavage sytem]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:26, 6 January 2021

OCA — Wed, 06 Jan 2021 09:26:50 GMT

←Older revision		Revision as of 09:26, 6 January 2021
Line 1:		Line 1:

	==Crystal Structure of Human T-protein of Glycine Cleavage System==		==Crystal Structure of Human T-protein of Glycine Cleavage System==
-	<StructureSection load='1wsr' size='340' side='right' caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1wsr' size='340' side='right'caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wsr]] 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WSR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wsr]] 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WSR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wsv\|1wsv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wsv\|1wsv]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([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/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://pdbe.org/1wsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsr 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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://pdbe.org/1wsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 35:		Line 35:

	==See Also==		==See Also==
-	*[[Aminomethyltransferase\|Aminomethyltransferase]]	+	*[[Aminomethyltransferase 3D structures\|Aminomethyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 42:		Line 42:
	[[Category: Aminomethyltransferase]]		[[Category: Aminomethyltransferase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Fujiwara, K]]		[[Category: Fujiwara, K]]
	[[Category: Hosaka, H]]		[[Category: Hosaka, H]]

OCA at 16:28, 11 April 2018

OCA — Wed, 11 Apr 2018 16:28:23 GMT

←Older revision		Revision as of 16:28, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Human T-protein of Glycine Cleavage System==		==Crystal Structure of Human T-protein of Glycine Cleavage System==
	<StructureSection load='1wsr' size='340' side='right' caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1wsr' size='340' side='right' caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([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/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://pdbe.org/1wsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr 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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://pdbe.org/1wsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 17:		Line 18:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ws/1wsr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ws/1wsr_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>

OCA at 17:14, 7 February 2016

OCA — Sun, 07 Feb 2016 17:14:57 GMT

←Older revision		Revision as of 17:14, 7 February 2016
Line 21:		Line 21:
	<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=1wsr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 32:
	</div>		</div>
	<div class="pdbe-citations 1wsr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wsr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminomethyltransferase\|Aminomethyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:32, 10 September 2015

OCA — Thu, 10 Sep 2015 03:32:53 GMT

←Older revision		Revision as of 03:32, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1wsr' size='340' side='right' caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1wsr' size='340' side='right' caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wsr]] is a 2 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WSR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wsr]] 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WSR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wsv\|1wsv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wsv\|1wsv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([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">GCST ([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/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr 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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://pdbe.org/1wsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 31:		Line 31:
	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 1wsr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Aminomethyltransferase]]		[[Category: Aminomethyltransferase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Fujiwara, K]]		[[Category: Fujiwara, K]]
	[[Category: Hosaka, H]]		[[Category: Hosaka, H]]

OCA at 13:48, 6 January 2015

OCA — Tue, 06 Jan 2015 13:48:50 GMT

←Older revision		Revision as of 13:48, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wsr]] is a 2 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WSR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wsr]] is a 2 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WSR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wsv\|1wsv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wsv\|1wsv]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([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">GCST ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr 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=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[http://omim.org/entry/605899 605899]]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref> <ref>PMID:9600239</ref> <ref>PMID:9621520</ref> <ref>PMID:10873393</ref> <ref>PMID:11286506</ref>		[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[http://omim.org/entry/605899 605899]]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref> <ref>PMID:9600239</ref> <ref>PMID:9621520</ref> <ref>PMID:10873393</ref> <ref>PMID:11286506</ref>
Line 37:		Line 37:
	[[Category: Aminomethyltransferase]]		[[Category: Aminomethyltransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Fujiwara, K.]]	+	[[Category: Fujiwara, K]]
-	[[Category: Hosaka, H.]]	+	[[Category: Hosaka, H]]
-	[[Category: Motokawa, Y.]]	+	[[Category: Motokawa, Y]]
-	[[Category: Nakagawa, A.]]	+	[[Category: Nakagawa, A]]
-	[[Category: Okamura-Ikeda, K.]]	+	[[Category: Okamura-Ikeda, K]]
-	[[Category: Taniguchi, H.]]	+	[[Category: Taniguchi, H]]
-	[[Category: Toma, S.]]	+	[[Category: Toma, S]]
-	[[Category: Yamashita, E.]]	+	[[Category: Yamashita, E]]
-	[[Category: Yoshimura, M.]]	+	[[Category: Yoshimura, M]]
	[[Category: Aminomethyl transferase]]		[[Category: Aminomethyl transferase]]
	[[Category: Glycine-cleavage sytem]]		[[Category: Glycine-cleavage sytem]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 21:59, 29 September 2014

OCA — Mon, 29 Sep 2014 21:59:10 GMT

←Older revision		Revision as of 21:59, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1wsr\| PDB=1wsr \| SCENE= }}~~	+	==Crystal Structure of Human T-protein of Glycine Cleavage System==
-	===Crystal Structure of Human T-protein of Glycine Cleavage System===	+	<StructureSection load='1wsr' size='340' side='right' caption='[[1wsr]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_16051266}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[1wsr]] is a 2 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=1WSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WSR FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
-	[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[http://omim.org/entry/605899 605899]]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref><ref>PMID:9600239</ref><ref>PMID:9621520</ref><ref>PMID:10873393</ref><ref>PMID:11286506</ref>	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wsv\|1wsv]]</td></tr>
-		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCST ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	==Function==	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wsr RCSB], [http://www.ebi.ac.uk/pdbsum/1wsr PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[http://omim.org/entry/605899 605899]]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref> <ref>PMID:9600239</ref> <ref>PMID:9621520</ref> <ref>PMID:10873393</ref> <ref>PMID:11286506</ref>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] The glycine cleavage system catalyzes the degradation of glycine.		[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] The glycine cleavage system catalyzes the degradation of glycine.
		+	== 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/ws/1wsr_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 ==
		+	T-protein, a component of the glycine cleavage system, catalyzes the formation of ammonia and 5,10-methylenetetrahydrofolate from the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein. Several mutations in the human T-protein gene cause non-ketotic hyperglycinemia. To gain insights into the effect of disease-causing mutations and the catalytic mechanism at the molecular level, crystal structures of human T-protein in free form and that bound to 5-methyltetrahydrofolate (5-CH3-H4folate) have been determined at 2.0 A and 2.6 A resolution, respectively. The overall structure consists of three domains arranged in a cloverleaf-like structure with the central cavity, where 5-CH3-H4folate is bound in a kinked shape with the pteridine group deeply buried into the hydrophobic pocket and the glutamyl group pointed to the C-terminal side surface. Most of the disease-related residues cluster around the cavity, forming extensive hydrogen bonding networks. These hydrogen bonding networks are employed in holding not only the folate-binding space but also the positions and the orientations of alpha-helix G and the following loop in the middle region, which seems to play a pivotal role in the T-protein catalysis. Structural and mutational analyses demonstrated that Arg292 interacts through water molecules with the folate polyglutamate tail, and that the invariant Asp101, located close to the N10 group of 5-CH3-H4folate, might play a key role in the initiation of the catalysis by increasing the nucleophilic character of the N10 atom of the folate substrate for the nucleophilic attack on the aminomethyl lipoate intermediate. A clever mechanism of recruiting the aminomethyl lipoate arm to the reaction site seems to function as a way of avoiding the release of toxic formaldehyde.

-	~~==About this Structure==~~	+	Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.,Okamura-Ikeda K, Hosaka H, Yoshimura M, Yamashita E, Toma S, Nakagawa A, Fujiwara K, Motokawa Y, Taniguchi H J Mol Biol. 2005 Sep 2;351(5):1146-59. PMID:16051266<ref>PMID:16051266</ref>
-	~~[[1wsr]] is a~~ 2 ~~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=1WSR OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:016051266</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aminomethyltransferase]]		[[Category: Aminomethyltransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 22:15, 24 March 2013

OCA — Sun, 24 Mar 2013 22:15:41 GMT

←Older revision		Revision as of 22:15, 24 March 2013
Line 1:		Line 1:
-	[[Image:1wsr.png\|left\|200px]]
-
	{{STRUCTURE_1wsr\| PDB=1wsr \| SCENE= }}		{{STRUCTURE_1wsr\| PDB=1wsr \| SCENE= }}
-
	===Crystal Structure of Human T-protein of Glycine Cleavage System===		===Crystal Structure of Human T-protein of Glycine Cleavage System===
		+	{{ABSTRACT_PUBMED_16051266}}

-	~~{{ABSTRACT_PUBMED_16051266}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[http://omim.org/entry/605899 605899]]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref><ref>PMID:9600239</ref><ref>PMID:9621520</ref><ref>PMID:10873393</ref><ref>PMID:11286506</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN]] The glycine cleavage system catalyzes the degradation of glycine.

	==About this Structure==		==About this Structure==
Line 11:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:016051266</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016051266</ref><references group="xtra"/><references/>
	[[Category: Aminomethyltransferase]]		[[Category: Aminomethyltransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA: Protected "1wsr" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 13:37:18 GMT

Protected "1wsr" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:37, 5 January 2013

OCA at 13:37, 5 January 2013

OCA — Sat, 05 Jan 2013 13:37:15 GMT

←Older revision		Revision as of 13:37, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wsr.png\|left\|200px]]		[[Image:1wsr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wsr", 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_1wsr\| PDB=1wsr \| SCENE= }}		{{STRUCTURE_1wsr\| PDB=1wsr \| SCENE= }}

	===Crystal Structure of Human T-protein of Glycine Cleavage System===		===Crystal Structure of Human T-protein of Glycine Cleavage System===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16051266}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16051266 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16051266}}		{{ABSTRACT_PUBMED_16051266}}

	==About this Structure==		==About this Structure==
-	~~1WSR~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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=1WSR OCA].	+	[[1wsr]] is a 2 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=1WSR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16051266~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016051266</ref><references group="xtra"/>
	[[Category: Aminomethyltransferase]]		[[Category: Aminomethyltransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 37:		Line 25:
	[[Category: Aminomethyl transferase]]		[[Category: Aminomethyl transferase]]
	[[Category: Glycine-cleavage sytem]]		[[Category: Glycine-cleavage sytem]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 15:22:06 2009''~~	+