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1zch

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Revision as of 09:02, 20 January 2021

Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis

Structural highlights

1zch is a 1 chain structure with sequence from "bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	ycnD ("Bacillus globigii" Migula 1900)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1zch"

@@ Line 1: / Line 1: @@
 ==Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis==
-<StructureSection load='1zch' size='340' side='right' caption='[[1zch]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<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 [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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZCH FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='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='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='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=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'>[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>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zc/1zch_consurf.spt"</scriptWhenChecked>
+    <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>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: Bacillus globigii migula 1900]]
+[[Category: Large Structures]]
 [[Category: Fitzpatrick, T B]]
 [[Category: Gruber, K]]

1zch

From Proteopedia

Revision as of 09:02, 20 January 2021

Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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