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| | <StructureSection load='1zch' size='340' side='right'caption='[[1zch]], [[Resolution|resolution]] 1.85Å' scene=''> | | <StructureSection load='1zch' size='340' side='right'caption='[[1zch]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1ZCH FirstGlance]. <br> | + | <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='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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ycnD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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'>[http://proteopedia.org/fgij/fg.htm?mol=1zch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zch OCA], [http://pdbe.org/1zch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zch RCSB], [http://www.ebi.ac.uk/pdbsum/1zch PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zch ProSAT]</span></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> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1zch" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1zch" style="background-color:#fffaf0;"></div> |
| - | | |
| - | ==See Also== | |
| - | *[[User:Andrzej Lyskowski|User:Andrzej Lyskowski]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Fitzpatrick, T B]] | + | [[Category: Fitzpatrick TB]] |
| - | [[Category: Gruber, K]] | + | [[Category: Gruber K]] |
| - | [[Category: Kratky, C]] | + | [[Category: Kratky C]] |
| - | [[Category: Lyskowski, A]] | + | [[Category: Lyskowski A]] |
| - | [[Category: Macheroux, P]] | + | [[Category: Macheroux P]] |
| - | [[Category: Morokutti, A]] | + | [[Category: Morokutti A]] |
| - | [[Category: Pointner, E]] | + | [[Category: Pointner E]] |
| - | [[Category: Sollner, S]] | + | [[Category: Sollner S]] |
| - | [[Category: Nadh-oxidase]]
| + | |
| - | [[Category: Nitroreductase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
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.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Morokutti A, Lyskowski A, Sollner S, Pointner E, Fitzpatrick TB, Kratky C, Gruber K, Macheroux P. Structure and function of YcnD from Bacillus subtilis, a flavin-containing oxidoreductase. Biochemistry. 2005 Oct 25;44(42):13724-33. PMID:16229462 doi:10.1021/bi0510835
- ↑ Morokutti A, Lyskowski A, Sollner S, Pointner E, Fitzpatrick TB, Kratky C, Gruber K, Macheroux P. Structure and function of YcnD from Bacillus subtilis, a flavin-containing oxidoreductase. Biochemistry. 2005 Oct 25;44(42):13724-33. PMID:16229462 doi:10.1021/bi0510835
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