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| | ==Crystal structure of oxidized YqjM from Bacillus subtilis complexed with p-hydroxybenzaldehyde== | | ==Crystal structure of oxidized YqjM from Bacillus subtilis complexed with p-hydroxybenzaldehyde== |
| - | <StructureSection load='1z42' size='340' side='right' caption='[[1z42]], [[Resolution|resolution]] 1.85Å' scene=''> | + | <StructureSection load='1z42' size='340' side='right'caption='[[1z42]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1z42]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z42 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1z42]] is a 2 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=1Z42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z42 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1z41|1z41]], [[1z44|1z44]], [[1z48|1z48]]</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=1z42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z42 OCA], [https://pdbe.org/1z42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z42 RCSB], [https://www.ebi.ac.uk/pdbsum/1z42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z42 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z42 OCA], [http://pdbe.org/1z42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z42 RCSB], [http://www.ebi.ac.uk/pdbsum/1z42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z42 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NAMA_BACSU NAMA_BACSU]] Catalyzes the reduction of the double bond of an array of alpha,beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes.<ref>PMID:12660247</ref> | + | [https://www.uniprot.org/uniprot/NAMA_BACSU NAMA_BACSU] Catalyzes the reduction of the double bond of an array of alpha,beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes.<ref>PMID:12660247</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Bourenkov, G P]] | + | [[Category: Large Structures]] |
| - | [[Category: Clausen, T]] | + | [[Category: Bourenkov GP]] |
| - | [[Category: Fitzpatrick, T B]] | + | [[Category: Clausen T]] |
| - | [[Category: Kitzing, K]] | + | [[Category: Fitzpatrick TB]] |
| - | [[Category: Macheroux, P]] | + | [[Category: Kitzing K]] |
| - | [[Category: Sawa, J]] | + | [[Category: Macheroux P]] |
| - | [[Category: Wilken, C]] | + | [[Category: Sawa J]] |
| - | [[Category: Beta-alpha-barrel]]
| + | [[Category: Wilken C]] |
| - | [[Category: Flavin]]
| + | |
| - | [[Category: Fmn]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: P-hydroxybenzaldehyde]]
| + | |
| Structural highlights
Function
NAMA_BACSU Catalyzes the reduction of the double bond of an array of alpha,beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes.[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
Here we report the crystal structure of YqjM, a homolog of Old Yellow Enzyme (OYE) that is involved in the oxidative stress response of Bacillus subtilis. In addition to the oxidized and reduced enzyme form, the structures of complexes with p-hydroxybenzaldehyde and p-nitrophenol, respectively, were solved. As for other OYE family members, YqjM folds into a (alpha/beta)8-barrel and has one molecule of flavin mononucleotide bound non-covalently at the COOH termini of the beta-sheet. Most of the interactions that control the electronic properties of the flavin mononucleotide cofactor are conserved within the OYE family. However, in contrast to all members of the OYE family characterized to date, YqjM exhibits several unique structural features. For example, the enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers. Moreover, the protein displays a shared active site architecture where an arginine finger (Arg336) at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal Tyr28 instead of a COOH-terminal tyrosine in OYE and its homologs. The structural information led to a specific data base search from which a new class of OYE oxidoreductases was identified that exhibits a strict conservation of active site residues, which are critical for this subfamily, most notably Cys26, Tyr28, Lys109, and Arg336. Therefore, YqjM is the first representative of a new bacterial subfamily of OYE homologs.
The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of Old Yellow Enzymes.,Kitzing K, Fitzpatrick TB, Wilken C, Sawa J, Bourenkov GP, Macheroux P, Clausen T J Biol Chem. 2005 Jul 29;280(30):27904-13. Epub 2005 May 12. PMID:15890652[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Fitzpatrick TB, Amrhein N, Macheroux P. Characterization of YqjM, an Old Yellow Enzyme homolog from Bacillus subtilis involved in the oxidative stress response. J Biol Chem. 2003 May 30;278(22):19891-7. Epub 2003 Mar 26. PMID:12660247 doi:http://dx.doi.org/10.1074/jbc.M211778200
- ↑ Kitzing K, Fitzpatrick TB, Wilken C, Sawa J, Bourenkov GP, Macheroux P, Clausen T. The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of Old Yellow Enzymes. J Biol Chem. 2005 Jul 29;280(30):27904-13. Epub 2005 May 12. PMID:15890652 doi:http://dx.doi.org/10.1074/jbc.M502587200
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