This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3wrb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:46, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of the anaerobic H124F DESb-Gallate complex==
==Crystal structure of the anaerobic H124F DESb-Gallate complex==
-
<StructureSection load='3wrb' size='340' side='right' caption='[[3wrb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+
<StructureSection load='3wrb' size='340' side='right'caption='[[3wrb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3wrb]] is a 2 chain structure with sequence from [http://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=3WRB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WRB FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3wrb]] 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=3WRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRB FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</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">[[3wku|3wku]], [[3wpm|3wpm]], [[3wr3|3wr3]], [[3wr4|3wr4]], [[3wr8|3wr8]], [[3wr9|3wr9]], [[3wra|3wra]], [[3wrc|3wrc]]</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>, <scene name='pdbligand=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">desB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13689 "Bacillus devorans" Zimmermann 1890])</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=3wrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wrb OCA], [https://pdbe.org/3wrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wrb RCSB], [https://www.ebi.ac.uk/pdbsum/3wrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wrb ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Linoleate_9S-lipoxygenase Linoleate 9S-lipoxygenase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wrb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wrb RCSB], [http://www.ebi.ac.uk/pdbsum/3wrb PDBsum]</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>
+
==See Also==
-
</div>
+
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacillus devorans zimmermann 1890]]
+
[[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]]
+

Current revision

Crystal structure of the anaerobic H124F DESb-Gallate complex

PDB ID 3wrb

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3wrb"
Personal tools