1s9a: Difference between revisions

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<StructureSection load='1s9a' size='340' side='right'caption='[[1s9a]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
<StructureSection load='1s9a' size='340' side='right'caption='[[1s9a]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1s9a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"nocardia_opaca"_aggag_and_schlegel_1973 "nocardia opaca" aggag and schlegel 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9A FirstGlance]. <br>
<table><tr><td colspan='2'>[[1s9a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_opacus Rhodococcus opacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HGP:(1-HEXADECANOYL-2-TETRADECANOYL-GLYCEROL-3-YL)+PHOSPHONYL+CHOLINE'>HGP</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</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]] 2.47&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HGP:(1-HEXADECANOYL-2-TETRADECANOYL-GLYCEROL-3-YL)+PHOSPHONYL+CHOLINE'>HGP</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</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=1s9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9a OCA], [https://pdbe.org/1s9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9a RCSB], [https://www.ebi.ac.uk/pdbsum/1s9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9a 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=1s9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9a OCA], [https://pdbe.org/1s9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9a RCSB], [https://www.ebi.ac.uk/pdbsum/1s9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CLCA_RHOOP CLCA_RHOOP]
== 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=1s9a 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=1s9a ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of the 4-chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium Rhodococcus opacus (erythropolis) 1CP, a Fe(III) ion-containing enzyme involved in the aerobic biodegradation of chloroaromatic compounds, has been solved by multiple wavelength anomalous dispersion using the weak anomalous signal of the two catalytic irons (1 Fe/257 amino acids) and refined at a 2.5 A resolution (R(free) 28.7%; R factor 21.4%). The analysis of the structure and its comparison with the structure of catechol 1,2-dioxygenase from Acinetobacter calcoaceticus ADP1 (Ac 1,2-CTD) highlight significant differences between these enzymes. The general topology of the present enzyme comprises two catalytic domains (one for each subunit) related by a noncrystallographic 2-fold axis and separated by a common alpha-helical zipper motif consisting of five N-terminal helices from each subunit; furthermore the C-terminal tail is shortened significantly with respect to the known Ac 1,2-CTD. The presence of two phospholipids binding in a hydrophobic tunnel along the dimer axis is shown here to be a common feature for this class of enzyme. The active site cavity presents several dissimilarities with respect to the known catechol-cleaving enzyme. The catalytic nonheme iron(III) ion is bound to the side chains of Tyr-134, Tyr-169, His-194, and His-196, and a cocrystallized benzoate ion, bound to the metal center, reveals details on a novel mode of binding of bidentate inhibitors and a distinctive hydrogen bond network with the surrounding ligands. Among the amino acid residues expected to interact with substrates, several are different from the corresponding analogs of Ac 1,2-CTD: Asp-52, Ala-53, Gly-76, Phe-78, and Cys-224; in addition, regions of largely conserved amino acid residues in the catalytic cleft show different shapes resulting from several substantial backbone and side chain shifts. The present structure is the first of intradiol dioxygenases that specifically catalyze the cleavage of chlorocatechols, key intermediates in the aerobic catabolism of toxic chloroaromatics.
Crystal structure of 4-chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing gram-positive Rhodococcus opacus 1CP.,Ferraroni M, Solyanikova IP, Kolomytseva MP, Scozzafava A, Golovleva L, Briganti F J Biol Chem. 2004 Jun 25;279(26):27646-55. Epub 2004 Apr 1. PMID:15060064<ref>PMID:15060064</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1s9a" 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: Nocardia opaca aggag and schlegel 1973]]
[[Category: Catechol 1,2-dioxygenase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Briganti, F]]
[[Category: Rhodococcus opacus]]
[[Category: Ferraroni, M]]
[[Category: Briganti F]]
[[Category: Golovleva, L A]]
[[Category: Ferraroni M]]
[[Category: Kolomytseva, M P]]
[[Category: Golovleva LA]]
[[Category: Scozzafava, A]]
[[Category: Kolomytseva MP]]
[[Category: Solyanikova, I P]]
[[Category: Scozzafava A]]
[[Category: Beta barrel]]
[[Category: Solyanikova IP]]
[[Category: Oxidoreductase]]

Latest revision as of 11:29, 14 February 2024

Crystal Structure of 4-Chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CPCrystal Structure of 4-Chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP

Structural highlights

1s9a is a 2 chain structure with sequence from Rhodococcus opacus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.47Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLCA_RHOOP

Evolutionary Conservation

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

See Also

1s9a, resolution 2.47Å

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