6on1: Difference between revisions

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<StructureSection load='6on1' size='340' side='right'caption='[[6on1]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
<StructureSection load='6on1' size='340' side='right'caption='[[6on1]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6on1]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ON1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6on1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sclerotialus Streptomyces sclerotialus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ON1 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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.982&#8491;</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=6on1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on1 OCA], [http://pdbe.org/6on1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6on1 RCSB], [http://www.ebi.ac.uk/pdbsum/6on1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6on1 ProSAT]</span></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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6on1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on1 OCA], [https://pdbe.org/6on1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6on1 RCSB], [https://www.ebi.ac.uk/pdbsum/6on1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6on1 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A5H1ZR51_9ACTN A0A5H1ZR51_9ACTN]
Extradiol dioxygenases are essential biocatalysts to breakdown catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. However, the VOC also contains an emerging class of biosynthetic dioxygenases. The L-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases are from pathways to various antibacterial or antitumor natural products, and their structural features are anticipated to be distinct from other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO), through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using a UV-vis spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 C, at which the Km and kcat of SsDDO were 110 +/- 10 muM and 2.0 +/- 0.1 s-1, respectively. We determined the de novo crystal structures of SsDDO in both the ligand-free form and as a substrate-bound complex, refined to 1.99 A and 2.31 A resolution, respectively. These structures reveal that SsDDO possesses a Form IV arrangement of betaalphabetabetabeta modules, the first characterization of this assembly from among the VOC/Type I extradiol dioxygenase protein family. EPR spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will expand our knowledge of the extradiol cleavage reaction within the VOC superfamily.


Crystal Structures of L-DOPA Dioxygenase from Streptomyces Sclerotialus.,Wang Y, Shin I, Fu Y, Colabroy KL, Liu A Biochemistry. 2019 Jun 10. doi: 10.1021/acs.biochem.9b00396. PMID:31180203<ref>PMID:31180203</ref>
==See Also==
 
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6on1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Colabroy, K]]
[[Category: Streptomyces sclerotialus]]
[[Category: Fu, Y]]
[[Category: Colabroy K]]
[[Category: Liu, A]]
[[Category: Fu Y]]
[[Category: Shin, I]]
[[Category: Liu A]]
[[Category: Wang, Y]]
[[Category: Shin I]]
[[Category: Extradiol dioxygenase]]
[[Category: Wang Y]]
[[Category: Oxidoreductase]]
[[Category: Vincinal oxygen chelate superfamily]]

Latest revision as of 17:52, 13 March 2024

A resting state structure of L-DOPA dioxygenase from Streptomyces sclerotialusA resting state structure of L-DOPA dioxygenase from Streptomyces sclerotialus

Structural highlights

6on1 is a 6 chain structure with sequence from Streptomyces sclerotialus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.982Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A5H1ZR51_9ACTN

See Also

6on1, resolution 1.98Å

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