1dlt: Difference between revisions

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<StructureSection load='1dlt' size='340' side='right'caption='[[1dlt]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='1dlt' size='340' side='right'caption='[[1dlt]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dlt]] 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=1DLT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DLT FirstGlance]. <br>
<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='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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dlm|1dlm]], [[1dlq|1dlq]], [[1dmh|1dmh]]</div></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='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=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>
<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>
</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]]
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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=1dlt 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=1dlt 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dlt" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
== References ==
*[[Thrombin 3D Structures|Thrombin 3D Structures]]
<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: Alpha/beta motif]]
[[Category: Aromatic hydrocarbon degredation]]
[[Category: Dioxygenase]]
[[Category: Metalloenzyme]]
[[Category: Oxidoreductase]]
[[Category: Substrate]]

Latest revision as of 09:55, 7 February 2024

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOLSTRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL

Structural highlights

1dlt is a 2 chain structure with sequence from Acinetobacter baylyi ADP1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CATA_ACIAD

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1dlt, resolution 1.90Å

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