3oum

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (02:14, 21 November 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3oum.jpg|left|200px]]
 
-
<!--
+
==Crystal Structure of toxoflavin-degrading enzyme in complex with toxoflavin==
-
The line below this paragraph, containing "STRUCTURE_3oum", creates the "Structure Box" on the page.
+
<StructureSection load='3oum' size='340' side='right'caption='[[3oum]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3oum]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OUM FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TOF:1,6-DIMETHYLPYRIMIDO[5,4-E][1,2,4]TRIAZINE-5,7(1H,6H)-DIONE'>TOF</scene></td></tr>
-
{{STRUCTURE_3oum| PDB=3oum | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3oum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oum OCA], [https://pdbe.org/3oum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oum RCSB], [https://www.ebi.ac.uk/pdbsum/3oum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oum ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/E3SET7_PAEPO E3SET7_PAEPO]
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 A in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis.
-
===Crystal Structure of toxoflavin-degrading enzyme in complex with toxoflavin===
+
Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme.,Jung WS, Lee J, Kim MI, Ma J, Nagamatsu T, Goo E, Kim H, Hwang I, Han J, Rhee S PLoS One. 2011;6(7):e22443. Epub 2011 Jul 25. PMID:21799856<ref>PMID:21799856</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_21799856}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3oum" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 21799856 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_21799856}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[3oum]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUM OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:021799856</ref><references group="xtra"/>
+
[[Category: Paenibacillus polymyxa]]
[[Category: Paenibacillus polymyxa]]
-
[[Category: Kim, M I.]]
+
[[Category: Kim MI]]
-
[[Category: Rhee, S.]]
+
[[Category: Rhee S]]
-
[[Category: Paenibacillus polymyxa jh2]]
+
-
[[Category: Phytotoxin-degrading enzyme]]
+
-
[[Category: Toxoflavin]]
+
-
[[Category: Toxoflavin binding protein]]
+
-
[[Category: Toxoflavin-degrading enzyme]]
+

Current revision

Crystal Structure of toxoflavin-degrading enzyme in complex with toxoflavin

PDB ID 3oum

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools