1c0p - Revision history

OCA at 06:40, 7 February 2024

OCA — Wed, 07 Feb 2024 06:40:13 GMT

←Older revision		Revision as of 06:40, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1c0p' size='340' side='right'caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1c0p' size='340' side='right'caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cbs_6016 Cbs 6016~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</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]] 1.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [https://pdbe.org/1c0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [https://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0p ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [https://pdbe.org/1c0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [https://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO]] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.	+	[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1c0p 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=1c0p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.
-
-	The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.,Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:11070076<ref>PMID:11070076</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1c0p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Amino acid oxidase 3D structures\|Amino acid oxidase 3D structures]]		*[[Amino acid oxidase 3D structures\|Amino acid oxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cbs 6016]]
-	[[Category: D-amino-acid oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Diederichs, K]]	+	[[Category: Rhodotorula toruloides]]
-	[[Category: Ghisla, S]]	+	[[Category: Diederichs K]]
-	[[Category: Molla, G]]	+	[[Category: Ghisla S]]
-	[[Category: Pilone~~, S M~~]]	+	[[Category: Molla G]]
-	[[Category: Pollegioni, L]]	+	[[Category: Pilone SM]]
-	[[Category: Umhau, S]]	+	[[Category: Pollegioni L]]
-	[[Category: Welte, W]]	+	[[Category: Umhau S]]
-	~~[[Category: Alpha-beta-alpha motif]]~~	+	[[Category: Welte W]]
-	~~[[Category: Flavin containing protein]]~~	+
-	~~[[Category: Oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:43, 28 April 2021

OCA — Wed, 28 Apr 2021 05:43:52 GMT

←Older revision		Revision as of 05:43, 28 April 2021
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	<StructureSection load='1c0p' size='340' side='right'caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1c0p' size='340' side='right'caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1C0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [~~http~~://pdbe.org/1c0p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0p ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [https://pdbe.org/1c0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [https://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO]] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.	+	[[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO]] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:31, 24 July 2019

OCA — Wed, 24 Jul 2019 06:31:52 GMT

←Older revision		Revision as of 06:31, 24 July 2019
Line 1:		Line 1:

	==D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES==		==D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES==
-	<StructureSection load='1c0p' size='340' side='right' caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>	+	<StructureSection load='1c0p' size='340' side='right'caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/1c0p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/1c0p_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1c0p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1c0p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Amino acid oxidase 3D structures\|Amino acid oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Cbs 6016]]		[[Category: Cbs 6016]]
	[[Category: D-amino-acid oxidase]]		[[Category: D-amino-acid oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]
	[[Category: Ghisla, S]]		[[Category: Ghisla, S]]

OCA at 08:03, 29 November 2017

OCA — Wed, 29 Nov 2017 08:03:29 GMT

←Older revision		Revision as of 08:03, 29 November 2017
Line 1:		Line 1:
		+
	==D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES==		==D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES==
	<StructureSection load='1c0p' size='340' side='right' caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1c0p' size='340' side='right' caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://pdbe.org/1c0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p 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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://pdbe.org/1c0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1c0p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1c0p" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Amino acid oxidase\|Amino acid oxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:34, 8 February 2016

OCA — Mon, 08 Feb 2016 10:34:25 GMT

←Older revision		Revision as of 10:34, 8 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=1c0p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:42, 10 September 2015

OCA — Thu, 10 Sep 2015 10:42:26 GMT

←Older revision		Revision as of 10:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1c0p' size='340' side='right' caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1c0p' size='340' side='right' caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodosporidium_toruloides Rhodosporidium toruloides~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p 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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://pdbe.org/1c0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1c0p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cbs 6016]]
	[[Category: D-amino-acid oxidase]]		[[Category: D-amino-acid oxidase]]
-	[[Category: Rhodosporidium toruloides]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]
	[[Category: Ghisla, S]]		[[Category: Ghisla, S]]

OCA at 22:42, 24 December 2014

OCA — Wed, 24 Dec 2014 22:42:37 GMT

←Older revision		Revision as of 22:42, 24 December 2014
Line 8:		Line 8:
	<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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p 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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO]] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:28, 22 December 2014

OCA — Mon, 22 Dec 2014 09:28:20 GMT

←Older revision		Revision as of 09:28, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p 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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: D-amino-acid oxidase]]		[[Category: D-amino-acid oxidase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]
-	[[Category: Diederichs, K.]]	+	[[Category: Diederichs, K]]
-	[[Category: Ghisla, S.]]	+	[[Category: Ghisla, S]]
-	[[Category: Molla, G.]]	+	[[Category: Molla, G]]
-	[[Category: Pilone, S M.]]	+	[[Category: Pilone, S M]]
-	[[Category: Pollegioni, L.]]	+	[[Category: Pollegioni, L]]
-	[[Category: Umhau, S.]]	+	[[Category: Umhau, S]]
-	[[Category: Welte, W.]]	+	[[Category: Welte, W]]
	[[Category: Alpha-beta-alpha motif]]		[[Category: Alpha-beta-alpha motif]]
	[[Category: Flavin containing protein]]		[[Category: Flavin containing protein]]
	[[Category: Oxidase]]		[[Category: Oxidase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 16:54, 20 August 2014

OCA — Wed, 20 Aug 2014 16:54:42 GMT

←Older revision		Revision as of 16:54, 20 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1c0p.~~png~~\|~~left~~\|200px]]	+	==D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES==
		+	<StructureSection load='1c0p' size='340' side='right' caption='[[1c0p]], [[Resolution\|resolution]] 1.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c0l\|1c0l]], [[1c0k\|1c0k]], [[1c0i\|1c0i]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [http://www.ebi.ac.uk/pdbsum/1c0p PDBsum]</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/c0/1c0p_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 ==
		+	Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.

-	~~{{STRUCTURE_1c0p\| PDB=1c0p \| SCENE= }}~~	+	The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.,Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:11070076<ref>PMID:11070076</ref>

-	~~===D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11070076}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1c0p]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA].~~	+

	==See Also==		==See Also==
	*[[Amino acid oxidase\|Amino acid oxidase]]		*[[Amino acid oxidase\|Amino acid oxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011070076<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: D-amino-acid oxidase]]		[[Category: D-amino-acid oxidase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]

OCA at 09:52, 20 October 2012

OCA — Sat, 20 Oct 2012 09:52:40 GMT

←Older revision		Revision as of 09:52, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1c0p]] is a 1 chain structure ~~of [[Amino acid oxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA].	+	[[1c0p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA].

	==See Also==		==See Also==