1dlm - Revision history

OCA at 06:55, 7 February 2024

OCA — Wed, 07 Feb 2024 06:55:44 GMT

←Older revision		Revision as of 06:55, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1dlm' size='340' side='right'caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1dlm' size='340' side='right'caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aciad Aciad~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baylyi_ADP1 Acinetobacter baylyi ADP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=LIO:~~[~~1-PENTADECANOYL-~~2~~-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</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;~~'>~~[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~https://en.wikipedia.org/wiki/Catechol_1,2~~-~~dioxygenase Catechol 1,~~2-~~dioxygenase], with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1~~] </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [https://pdbe.org/1dlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [https://www.ebi.ac.uk/pdbsum/1dlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dlm 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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [https://pdbe.org/1dlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [https://www.ebi.ac.uk/pdbsum/1dlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dlm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CATA_ACIAD CATA_ACIAD]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		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=1dlm 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=1dlm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1, 2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(2-12). RESULTS: The crystal structure of 1,2-CTD from Acinetobacter sp. ADP1 (Ac 1,2-CTD) was solved by single isomorphous replacement and refined to 2.0 A resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 A and 1.8 A, respectively. While the characteristics of the iron ligands are similar, Ac 1,2-CTD differs from 3,4-PCDs in that only one subunit is used to fashion each active-site cavity. In addition, a novel 'helical zipper', consisting of five N-terminal helices from each subunit, forms the molecular dimer axis. Two phospholipids were unexpectedly found to bind within an 8 x 35 A hydrophobic tunnel along this axis. CONCLUSIONS: The helical zipper domain of Ac 1, 2-CTD has no equivalent in other proteins of known structure. Sequence analysis suggests the domain is a common motif in all members of the 1,2-CTD family. Complexes with catechol and 4-methylcatechol are the highest resolution complex structures to date of an intradiol dioxygenase. Furthermore, they confirm several observations seen in 3,4-PCDs, including ligand displacement upon binding exogenous ligands. The structures presented here are the first of a new family of intradiol dioxygenases.
-
-	The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.,Vetting MW, Ohlendorf DH Structure. 2000 Apr 15;8(4):429-40. PMID:10801478<ref>PMID:10801478</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dlm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciad]]~~	+	[[Category: Acinetobacter baylyi ADP1]]
-	~~[[Category: Catechol 1,2-dioxygenase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ohlendorf~~, D H~~]]	+	[[Category: Ohlendorf DH]]
-	[[Category: Vetting~~, M W]]~~	+	[[Category: Vetting MW]]
-	~~[[Category: Aromatic compound degradation]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Metalloprotein]]~~	+
-	~~[[Category: Mixed alpha helix/ beta strand]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 18:29, 10 March 2021

OCA — Wed, 10 Mar 2021 18:29:43 GMT

←Older revision		Revision as of 18:29, 10 March 2021
Line 3:		Line 3:
	<StructureSection load='1dlm' size='340' side='right'caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1dlm' size='340' side='right'caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [~~http~~://pdbe.org/1dlm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dlm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dlm 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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [https://pdbe.org/1dlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [https://www.ebi.ac.uk/pdbsum/1dlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dlm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:49, 5 June 2019

OCA — Wed, 05 Jun 2019 23:49:38 GMT

←Older revision		Revision as of 23:49, 5 June 2019
Line 1:		Line 1:

	==STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA==		==STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA==
-	<StructureSection load='1dlm' size='340' side='right' caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1dlm' size='340' side='right'caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/1dlm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/1dlm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aciad]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Ohlendorf, D H]]		[[Category: Ohlendorf, D H]]
	[[Category: Vetting, M W]]		[[Category: Vetting, M W]]

OCA at 04:15, 30 August 2017

OCA — Wed, 30 Aug 2017 04:15:59 GMT

←Older revision		Revision as of 04:15, 30 August 2017
Line 1:		Line 1:
		+
	==STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA==		==STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA==
	<StructureSection load='1dlm' size='340' side='right' caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1dlm' size='340' side='right' caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Aciad Aciad]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://pdbe.org/1dlm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm 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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://pdbe.org/1dlm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dlm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=1dlm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aciad]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]
	[[Category: Ohlendorf, D H]]		[[Category: Ohlendorf, D H]]

OCA at 10:40, 11 September 2015

OCA — Fri, 11 Sep 2015 10:40:30 GMT

←Older revision		Revision as of 10:40, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1dlm' size='340' side='right' caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1dlm' size='340' side='right' caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Acinetobacter_sp. Acinetobacter sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm 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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://pdbe.org/1dlm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1dlm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acinetobacter sp~~]]	+	[[Category: Aciad]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]
	[[Category: Ohlendorf, D H]]		[[Category: Ohlendorf, D H]]

OCA at 18:34, 22 December 2014

OCA — Mon, 22 Dec 2014 18:34:41 GMT

←Older revision		Revision as of 18:34, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm 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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm 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 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Acinetobacter sp.]]	+	[[Category: Acinetobacter sp]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]
-	[[Category: Ohlendorf, D H.]]	+	[[Category: Ohlendorf, D H]]
-	[[Category: Vetting, M W.]]	+	[[Category: Vetting, M W]]
	[[Category: Aromatic compound degradation]]		[[Category: Aromatic compound degradation]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]

OCA at 06:46, 4 September 2014

OCA — Thu, 04 Sep 2014 06:46:57 GMT

←Older revision		Revision as of 06:46, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dlm.~~png~~\|~~left~~\|200px]]	+	==STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA==
		+	<StructureSection load='1dlm' size='340' side='right' caption='[[1dlm]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DLM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LIO:[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL+CHOLINE'>LIO</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlq\|1dlq]], [[1dlt\|1dlt]], [[1dmh\|1dmh]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] </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=1dlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dlm RCSB], [http://www.ebi.ac.uk/pdbsum/1dlm 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/dl/1dlm_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 ==
		+	BACKGROUND: Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1, 2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(2-12). RESULTS: The crystal structure of 1,2-CTD from Acinetobacter sp. ADP1 (Ac 1,2-CTD) was solved by single isomorphous replacement and refined to 2.0 A resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 A and 1.8 A, respectively. While the characteristics of the iron ligands are similar, Ac 1,2-CTD differs from 3,4-PCDs in that only one subunit is used to fashion each active-site cavity. In addition, a novel 'helical zipper', consisting of five N-terminal helices from each subunit, forms the molecular dimer axis. Two phospholipids were unexpectedly found to bind within an 8 x 35 A hydrophobic tunnel along this axis. CONCLUSIONS: The helical zipper domain of Ac 1, 2-CTD has no equivalent in other proteins of known structure. Sequence analysis suggests the domain is a common motif in all members of the 1,2-CTD family. Complexes with catechol and 4-methylcatechol are the highest resolution complex structures to date of an intradiol dioxygenase. Furthermore, they confirm several observations seen in 3,4-PCDs, including ligand displacement upon binding exogenous ligands. The structures presented here are the first of a new family of intradiol dioxygenases.

-	~~{{STRUCTURE_1dlm\| PDB=1dlm \| SCENE= }}~~	+	The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.,Vetting MW, Ohlendorf DH Structure. 2000 Apr 15;8(4):429-40. PMID:10801478<ref>PMID:10801478</ref>

-	~~===STRUCTURE OF CATECHOL 1~~,~~2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_10801478}}~~	+	==See Also==
-		+	*[[Dioxygenase\|Dioxygenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1dlm~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:010801478<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Acinetobacter sp.]]		[[Category: Acinetobacter sp.]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]

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

OCA — Wed, 31 Oct 2012 10:03:12 GMT

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

←Older revision

Revision as of 10:03, 31 October 2012

OCA at 10:03, 31 October 2012

OCA — Wed, 31 Oct 2012 10:03:10 GMT

←Older revision		Revision as of 10:03, 31 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1dlm.png\|left\|200px]]		[[Image:1dlm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1dlm", 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_1dlm\| PDB=1dlm \| SCENE= }}		{{STRUCTURE_1dlm\| PDB=1dlm \| SCENE= }}

	===STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA===		===STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10801478}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10801478 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10801478}}		{{ABSTRACT_PUBMED_10801478}}

	==About this Structure==		==About this Structure==
-	~~1DLM~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA].	+	[[1dlm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10801478~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010801478</ref><references group="xtra"/>
	[[Category: Acinetobacter sp.]]		[[Category: Acinetobacter sp.]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]
Line 32:		Line 20:
	[[Category: Metalloprotein]]		[[Category: Metalloprotein]]
	[[Category: Mixed alpha helix/ beta strand]]		[[Category: Mixed alpha helix/ beta strand]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 20:09:37 2009''~~	+

OCA at 18:09, 17 February 2009

OCA — Tue, 17 Feb 2009 18:09:39 GMT

←Older revision		Revision as of 18:09, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1DLM is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA].	+	1DLM is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLM OCA].

	==Reference==		==Reference==
-	~~The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker., Vetting MW, Ohlendorf DH, Structure. 2000 Apr 15;8(4):429-40.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10801478 10801478]~~	+	<ref group="xtra">PMID:10801478</ref><references group="xtra"/>
	[[Category: Acinetobacter sp.]]		[[Category: Acinetobacter sp.]]
	[[Category: Catechol 1,2-dioxygenase]]		[[Category: Catechol 1,2-dioxygenase]]
-	[[Category: Single protein]]
	[[Category: Ohlendorf, D H.]]		[[Category: Ohlendorf, D H.]]
	[[Category: Vetting, M W.]]		[[Category: Vetting, M W.]]
Line 34:		Line 33:
	[[Category: Mixed alpha helix/ beta strand]]		[[Category: Mixed alpha helix/ beta strand]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jun 30 23~~:15:~~25 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:09:37 2009''