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| [[Image:1dlt.gif|left|200px]]<br /><applet load="1dlt" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1dlt, resolution 1.9Å" />
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| '''STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL'''<br />
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| ==Overview== | | ==STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL== |
| 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.
| | <StructureSection load='1dlt' size='340' side='right'caption='[[1dlt]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[1dlt]] 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=1DLT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DLT FirstGlance]. <br> |
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dlt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dlt OCA], [https://pdbe.org/1dlt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dlt RCSB], [https://www.ebi.ac.uk/pdbsum/1dlt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dlt ProSAT]</span></td></tr> |
| | </table> |
| | == Function == |
| | [https://www.uniprot.org/uniprot/CATA_ACIAD CATA_ACIAD] |
| | == 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/1dlt_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/main_output.php?pdb_ID=1dlt ConSurf]. |
| | <div style="clear:both"></div> |
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| ==About this Structure== | | ==See Also== |
| 1DLT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.] with <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=CAQ:'>CAQ</scene> and <scene name='pdbligand=LIO:'>LIO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLT OCA].
| | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| | | *[[Thrombin 3D Structures|Thrombin 3D Structures]] |
| ==Reference==
| | __TOC__ |
| 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10801478 10801478]
| | </StructureSection> |
| [[Category: Acinetobacter sp.]] | | [[Category: Acinetobacter baylyi ADP1]] |
| [[Category: Catechol 1,2-dioxygenase]]
| | [[Category: Large Structures]] |
| [[Category: Single protein]] | | [[Category: Ohlendorf DH]] |
| [[Category: Ohlendorf, D H.]] | | [[Category: Vetting MW]] |
| [[Category: Vetting, M W.]] | |
| [[Category: CAQ]]
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| [[Category: FE]]
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| [[Category: LIO]]
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| [[Category: alpha/beta motif]]
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| [[Category: aromatic hydrocarbon degredation]]
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| [[Category: dioxygenase]]
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| [[Category: metalloenzyme]]
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| [[Category: substrate]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:55 2008''
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