2igk: Difference between revisions

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{{Seed}}
[[Image:2igk.png|left|200px]]


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==Crystal structure of recombinant pyranose 2-oxidase==
The line below this paragraph, containing "STRUCTURE_2igk", creates the "Structure Box" on the page.
<StructureSection load='2igk' size='340' side='right'caption='[[2igk]], [[Resolution|resolution]] 1.80&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'>[[2igk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IGK 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]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
{{STRUCTURE_2igk|  PDB=2igk  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2igk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2igk OCA], [https://pdbe.org/2igk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2igk RCSB], [https://www.ebi.ac.uk/pdbsum/2igk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2igk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q7ZA32_TRAOC Q7ZA32_TRAOC]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/2igk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2igk ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyranose 2-oxidase (P2Ox) participates in fungal lignin degradation by producing the H2O2 needed for lignin-degrading peroxidases. The enzyme oxidizes cellulose- and hemicellulose-derived aldopyranoses at C2 preferentially, but also on C3, to the corresponding ketoaldoses. To investigate the structural determinants of catalysis, covalent flavinylation, substrate binding, and regioselectivity, wild-type and mutant P2Ox enzymes were produced and characterized biochemically and structurally. Removal of the histidyl-FAD linkage resulted in a catalytically competent enzyme containing tightly, but noncovalently bound FAD. This mutant (H167A) is characterized by a 5-fold lower kcat, and a 35-mV lower redox potential, although no significant structural changes were seen in its crystal structure. In previous structures of P2Ox, the substrate loop (residues 452-457) covering the active site has been either disordered or in a conformation incompatible with carbohydrate binding. We present here the crystal structure of H167A in complex with a slow substrate, 2-fluoro-2-deoxy-D-glucose. Based on the details of 2-fluoro-2-deoxy-D-glucose binding in position for oxidation at C3, we also outline a probable binding mode for D-glucose positioned for regioselective oxidation at C2. The tentative determinant for discriminating between the two binding modes is the position of the O6 hydroxyl group, which in the C2-oxidation mode can make favorable interactions with Asp452 in the substrate loop and, possibly, a nearby arginine residue (Arg472). We also substantiate our hypothesis with steady-state kinetics data for the alanine replacements of Asp452 and Arg472 as well as the double alanine 452/472 mutant.


===Crystal structure of recombinant pyranose 2-oxidase===
Structural basis for substrate binding and regioselective oxidation of monosaccharides at C3 by pyranose 2-oxidase.,Kujawa M, Ebner H, Leitner C, Hallberg BM, Prongjit M, Sucharitakul J, Ludwig R, Rudsander U, Peterbauer C, Chaiyen P, Haltrich D, Divne C J Biol Chem. 2006 Nov 17;281(46):35104-15. Epub 2006 Sep 19. PMID:16984920<ref>PMID:16984920</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2igk" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_16984920}}, adds the Publication Abstract to the page
*[[Pyranose oxidase|Pyranose oxidase]]
(as it appears on PubMed at http://www.pubmed.gov), where 16984920 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_16984920}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2IGK is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGK OCA].
 
==Reference==
<ref group="xtra">PMID:16984920</ref><references group="xtra"/>
[[Category: Pyranose oxidase]]
[[Category: Trametes ochracea]]
[[Category: Trametes ochracea]]
[[Category: Divne, C.]]
[[Category: Divne C]]
[[Category: Gmc oxidoreductase]]
[[Category: Homotetramer]]
[[Category: Oxidoreductase]]
[[Category: Phbh fold]]
[[Category: Rossman fold]]
 
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Retrieved from "https://proteopedia.org/2igk"