3wra: Difference between revisions

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<StructureSection load='3wra' size='340' side='right'caption='[[3wra]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='3wra' size='340' side='right'caption='[[3wra]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3wra]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRA FirstGlance]. <br>
<table><tr><td colspan='2'>[[3wra]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRA FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 2.1&#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;'>[[3wku|3wku]], [[3wpm|3wpm]], [[3wr3|3wr3]], [[3wr4|3wr4]], [[3wr8|3wr8]], [[3wr9|3wr9]], [[3wrb|3wrb]], [[3wrc|3wrc]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">desB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13689 "Bacillus devorans" Zimmermann 1890])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Linoleate_9S-lipoxygenase Linoleate 9S-lipoxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.58 1.13.11.58] </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=3wra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wra OCA], [https://pdbe.org/3wra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wra RCSB], [https://www.ebi.ac.uk/pdbsum/3wra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wra 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=3wra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wra OCA], [https://pdbe.org/3wra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wra RCSB], [https://www.ebi.ac.uk/pdbsum/3wra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wra ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/G2IKE5_SPHSK G2IKE5_SPHSK]
DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5) of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.
 
Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6.,Sugimoto K, Senda M, Kasai D, Fukuda M, Masai E, Senda T PLoS One. 2014 Mar 21;9(3):e92249. doi: 10.1371/journal.pone.0092249. eCollection, 2014. PMID:24657997<ref>PMID:24657997</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3wra" 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: Bacillus devorans zimmermann 1890]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Linoleate 9S-lipoxygenase]]
[[Category: Sphingomonas paucimobilis]]
[[Category: Fukuda, M]]
[[Category: Fukuda M]]
[[Category: Kasai, D]]
[[Category: Kasai D]]
[[Category: Masai, E]]
[[Category: Masai E]]
[[Category: Senda, M]]
[[Category: Senda M]]
[[Category: Senda, T]]
[[Category: Senda T]]
[[Category: Sugimoto, K]]
[[Category: Sugimoto K]]
[[Category: Domain-swap dimer]]
[[Category: Extradiol dioxygenase]]
[[Category: Fe2+ binding]]
[[Category: Oxidoreductase]]

Latest revision as of 11:46, 20 March 2024

Crystal structure of the desB-Gallate complex exposed to Aerobic AtomosphereCrystal structure of the desB-Gallate complex exposed to Aerobic Atomosphere

Structural highlights

3wra is a 2 chain structure with sequence from Sphingomonas paucimobilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G2IKE5_SPHSK

See Also

3wra, resolution 2.10Å

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OCA
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