3wpm: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of the anaerobic DesB-gallate complex by co-crystallization== | ==Crystal structure of the anaerobic DesB-gallate complex by co-crystallization== | ||
<StructureSection load='3wpm' size='340' side='right' caption='[[3wpm]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='3wpm' size='340' side='right'caption='[[3wpm]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3wpm]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3wpm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphsk Sphsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WPM 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=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</scene></td></tr> | </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=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vju|3vju]], [[3vjv|3vjv]], [[3vjw|3vjw]], [[3vjx|3vjx]], [[3vjy|3vjy]], [[3wku|3wku]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vju|3vju]], [[3vjv|3vjv]], [[3vjw|3vjw]], [[3vjx|3vjx]], [[3vjy|3vjy]], [[3wku|3wku]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">desB ([ | <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=627192 SPHSK])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wpm OCA], [https://pdbe.org/3wpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wpm RCSB], [https://www.ebi.ac.uk/pdbsum/3wpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wpm ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 20: | Line 20: | ||
==See Also== | ==See Also== | ||
*[[Dioxygenase|Dioxygenase]] | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Sphsk]] | |||
[[Category: Fukuda, M]] | [[Category: Fukuda, M]] | ||
[[Category: Kasai, D]] | [[Category: Kasai, D]] | ||
Revision as of 08:45, 3 August 2022
Crystal structure of the anaerobic DesB-gallate complex by co-crystallizationCrystal structure of the anaerobic DesB-gallate complex by co-crystallization
Structural highlights
Publication Abstract from PubMedDesB, 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||