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==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 ==
[[3wrb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRB OCA]. <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>
<b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</scene><br>
</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>
<b>[[Related_structure|Related:]]</b> [[3wku|3wku]], [[3wpm|3wpm]], [[3wr3|3wr3]], [[3wr4|3wr4]], [[3wr8|3wr8]], [[3wr9|3wr9]], [[3wra|3wra]], [[3wrc|3wrc]]<br>
<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>
<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
<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>
<b>Resources:</b> <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><br>
</table>
== Publication Abstract from PubMed ==
== Function ==
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.
[https://www.uniprot.org/uniprot/G2IKE5_SPHSK G2IKE5_SPHSK]
 
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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
==See Also==
== References ==
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Linoleate 9S-lipoxygenase]]
[[Category: Large Structures]]
[[Category: Fukuda, M.]]
[[Category: Sphingomonas paucimobilis]]
[[Category: Kasai, D.]]
[[Category: Fukuda M]]
[[Category: Masai, E.]]
[[Category: Kasai D]]
[[Category: Senda, M.]]
[[Category: Masai E]]
[[Category: Senda, T.]]
[[Category: Senda M]]
[[Category: Sugimoto, K.]]
[[Category: Senda T]]
[[Category: Domain-swap dimer]]
[[Category: Sugimoto K]]
[[Category: Extradiol dioxygenase]]
[[Category: Fe2+ binding]]
[[Category: Oxidoreductase]]

Latest revision as of 11:46, 20 March 2024

Crystal structure of the anaerobic H124F DESb-Gallate complexCrystal structure of the anaerobic H124F DESb-Gallate complex

Structural highlights

3wrb 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

3wrb, resolution 2.10Å

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