View source for 1zch


==Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis==
<StructureSection load='1zch' size='340' side='right'caption='[[1zch]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1zch]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZCH FirstGlance]. <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]] 1.85&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></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=1zch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zch OCA], [https://pdbe.org/1zch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zch RCSB], [https://www.ebi.ac.uk/pdbsum/1zch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zch ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NFRA2_BACSU NFRA2_BACSU] Reduces FMNH(2) to FMN, with NADH or NADPH as reductant. It also reduces nitroaromatic compounds, quinones, chromates and azo dyes. It could supply the reduced form of FMN to luciferase-like protein and contribute to the degradation of aromatic compounds.<ref>PMID:16229462</ref> 
== 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/zc/1zch_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1zch ConSurf].
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== Publication Abstract from PubMed ==
YcnD from the gram-positive bacterium Bacillus subtilis is a member of a family of bacterial proteins that act as NADH- and/or NADPH-dependent oxidoreductases. Here, we report for the first time on the biochemical characterization of the purified protein, demonstrating that YcnD is an FMN-containing enzyme that can be reduced by NADH or NADPH (Km = 6.4 and 4.4 microM, respectively). In the presence of free FMN as the electron-accepting substrate, the latter reductant showed a ping-pong Bi-Bi reaction mechanism, whereas utilization of NADH is competitively inhibited by this substrate. This finding suggests that NADPH is the physiological reductant of the enzyme. We also show that YcnD reduces nitro-organic compounds, chromate, and a series of azo dyes. The reduction of azo dyes appears to be mediated by free reduced FMN because the reaction is considerably slower in its absence. Structure determination by X-ray crystallography revealed that YcnD folds into a three layer alpha-beta-alpha sandwich strongly resembling the topology of the NADH oxidase superfamily. Similar to homologous bacterial oxidoreductase, YcnD forms homodimers with an extended dimer interface. The biochemical data and the structure are discussed in light of the putative physiological function of YcnD as an oxidoreductase delivering reduced FMN to enzymes that require the reduced cofactor for activity.

Structure and function of YcnD from Bacillus subtilis, a flavin-containing oxidoreductase.,Morokutti A, Lyskowski A, Sollner S, Pointner E, Fitzpatrick TB, Kratky C, Gruber K, Macheroux P Biochemistry. 2005 Oct 25;44(42):13724-33. PMID:16229462<ref>PMID:16229462</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1zch" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Fitzpatrick TB]]
[[Category: Gruber K]]
[[Category: Kratky C]]
[[Category: Lyskowski A]]
[[Category: Macheroux P]]
[[Category: Morokutti A]]
[[Category: Pointner E]]
[[Category: Sollner S]]