1wyv - Revision history

OCA at 13:35, 13 March 2024

OCA — Wed, 13 Mar 2024 13:35:20 GMT

←Older revision		Revision as of 13:35, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wyv' size='340' side='right'caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1wyv' size='340' side='right'caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1WYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>~~, ~~<scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1wyt\|1wyt]], [[1wyu\|1wyu]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [https://pdbe.org/1wyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [https://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [https://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</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_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </~~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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [~~http~~://pdbe.org/1wyv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5SKW8_THET8 Q5SKW8_THET8] The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity).[HAMAP-Rule:MF_00712][SAAS:SAAS023010_004_045580]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1wyv 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=1wyv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.
-
-	Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.,Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207<ref>PMID:15791207</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wyv" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Kamiya, N]]	+	[[Category: Kamiya N]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Kuramitsu S]]
-	[[Category: Maoka, N]]	+	[[Category: Maoka N]]
-	[[Category: Masui, R]]	+	[[Category: Masui R]]
-	[[Category: Nakagawa, N]]	+	[[Category: Nakagawa N]]
-	[[Category: Nakai, T]]	+	[[Category: Nakai T]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 09:32, 6 January 2021

OCA — Wed, 06 Jan 2021 09:32:16 GMT

←Older revision		Revision as of 09:32, 6 January 2021
Line 1:		Line 1:

	==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==		==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==
-	<StructureSection load='1wyv' size='340' side='right' caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1wyv' size='340' side='right'caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wyt\|1wyt]], [[1wyu\|1wyu]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://pdbe.org/1wyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://pdbe.org/1wyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet8]]		[[Category: Thet8]]
	[[Category: Kamiya, N]]		[[Category: Kamiya, N]]

OCA at 16:12, 11 April 2018

OCA — Wed, 11 Apr 2018 16:12:13 GMT

OCA at 23:37, 9 February 2016

OCA — Tue, 09 Feb 2016 23:37:42 GMT

←Older revision		Revision as of 23:37, 9 February 2016
Line 18:		Line 18:
	<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=1wyv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:11, 11 September 2015

OCA — Fri, 11 Sep 2015 03:11:21 GMT

←Older revision		Revision as of 03:11, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1wyv' size='340' side='right' caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1wyv' size='340' side='right' caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~274 Thermus thermophilus~~]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~274 Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://pdbe.org/1wyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	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 1wyv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Thet8]]
	[[Category: Kamiya, N]]		[[Category: Kamiya, N]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 12:35, 6 January 2015

OCA — Tue, 06 Jan 2015 12:35:11 GMT

←Older revision		Revision as of 12:35, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Kamiya, N.]]	+	[[Category: Kamiya, N]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Maoka, N.]]	+	[[Category: Maoka, N]]
-	[[Category: Masui, R.]]	+	[[Category: Masui, R]]
-	[[Category: Nakagawa, N.]]	+	[[Category: Nakagawa, N]]
-	[[Category: Nakai, T.]]	+	[[Category: Nakai, T]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 21:24, 29 September 2014

OCA — Mon, 29 Sep 2014 21:24:11 GMT

←Older revision		Revision as of 21:24, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wyv.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==
		+	<StructureSection load='1wyv' size='340' side='right' caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
		+	<table>
		+	== 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/wy/1wyv_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 ==
		+	The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.

-	~~{{STRUCTURE_1wyv\| PDB=1wyv \| SCENE= }}~~	+	Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.,Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207<ref>PMID:15791207</ref>

-	~~===Crystal structure of glycine decarboxylase (P-protein)~~ of the ~~glycine cleavage system, in inhibitor-bound form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15791207}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1wyv]] is a 8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015791207<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N.]]

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

OCA — Sat, 05 Jan 2013 12:36:52 GMT

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

←Older revision

Revision as of 12:36, 5 January 2013

OCA at 12:36, 5 January 2013

OCA — Sat, 05 Jan 2013 12:36:47 GMT

←Older revision		Revision as of 12:36, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wyv.png\|left\|200px]]		[[Image:1wyv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wyv", 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_1wyv\| PDB=1wyv \| SCENE= }}		{{STRUCTURE_1wyv\| PDB=1wyv \| SCENE= }}

	===Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form===		===Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15791207}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15791207 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15791207}}		{{ABSTRACT_PUBMED_15791207}}

	==About this Structure==		==About this Structure==
-	~~1WYV~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA].	+	[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15791207~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015791207</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N.]]
Line 32:		Line 20:
	[[Category: Nakai, T.]]		[[Category: Nakai, T.]]
	[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]		[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
		+	[[Category: Oxidoreductase]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:39:22 2009''

OCA at 11:39, 17 February 2009

OCA — Tue, 17 Feb 2009 11:39:23 GMT

←Older revision		Revision as of 11:39, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia., Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N, EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15791207 15791207]~~	+	<ref group="xtra">PMID:15791207</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N.]]
Line 36:		Line 36:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16~~ 17:06:~~56 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:39:22 2009''

←Older revision		Revision as of 16:12, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==		==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==
	<StructureSection load='1wyv' size='340' side='right' caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1wyv' size='340' side='right' caption='[[1wyv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wyv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PLP~~:~~PYRIDOXAL-5-PHOSPHATE~~'>~~PLP~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~AOA~~:~~(AMINOOXY)ACETIC+ACID~~'>~~AOA~~</scene></td></tr>	+
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyt\|1wyt]], [[1wyu\|1wyu]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://pdbe.org/1wyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</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=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [http://pdbe.org/1wyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [http://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [http://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyv_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>