3d3f

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis

Structural highlights

3d3f is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GR_BACSU Reduces glyoxal and methylglyoxal. Is not involved in the vitamin B6 biosynthesis.

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

Bacillus subtilis is one of the most studied gram-positive bacteria. In this work, YvgN and YtbE from B. subtilis, assigned as AKR5G1 and AKR5G2 of aldo-keto reductase (AKR) superfamily. AKR catalyzes the NADPH-dependent reduction of aldehyde or aldose substrates to alcohols. YvgN and YtbE were studied by crystallographic and enzymatic analyses. The apo structures of these proteins were determined by molecular replacement, and the structure of holoenzyme YvgN with NADPH was also solved, revealing the conformational changes upon cofactor binding. Our biochemical data suggest both YvgN and YtbE have preferential specificity for derivatives of benzaldehyde, such as nitryl or halogen group substitution at the 2 or 4 positions. These proteins also showed broad catalytic activity on many standard substrates of AKR, such as glyoxal, dihydroxyacetone, and DL-glyceraldehyde, suggesting a possible role in bacterial detoxification.

Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis.,Lei J, Zhou YF, Li LF, Su XD Protein Sci. 2009 Aug;18(8):1792-800. PMID:19585557^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lei J, Zhou YF, Li LF, Su XD. Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis. Protein Sci. 2009 Aug;18(8):1792-800. PMID:19585557 doi:http://dx.doi.org/10.1002/pro.178

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3d3f"

Categories: Bacillus subtilis | Large Structures | Lei J | Su XD | Zhou YF

@@ Line 3: / Line 3: @@
 <StructureSection load='3d3f' size='340' side='right'caption='[[3d3f]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3d3f]] is a 2 chain structure with sequence from [https://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=3D3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3d3f]] 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=3D3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D3F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 2.4&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yvgN ([https://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=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=3d3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3f OCA], [https://pdbe.org/3d3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d3f RCSB], [https://www.ebi.ac.uk/pdbsum/3d3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d3f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GR_BACSU GR_BACSU]] Reduces glyoxal and methylglyoxal. Is not involved in the vitamin B6 biosynthesis.
+[https://www.uniprot.org/uniprot/GR_BACSU GR_BACSU] Reduces glyoxal and methylglyoxal. Is not involved in the vitamin B6 biosynthesis.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus globigii migula 1900]]
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Lei, J]]
+[[Category: Lei J]]
-[[Category: Su, X D]]
+[[Category: Su XD]]
-[[Category: Zhou, Y F]]
+[[Category: Zhou YF]]
-[[Category: Aldo-keto reductase]]
-[[Category: Oxidoreductase]]

3d3f

From Proteopedia

Current revision

Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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