3d3f

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:03, 1 November 2023) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
-
{{STRUCTURE_3d3f| PDB=3d3f | SCENE= }}
 
-
===Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis===
 
-
{{ABSTRACT_PUBMED_19585557}}
 
-
==Function==
+
==Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis==
-
[[http://www.uniprot.org/uniprot/GR_BACSU GR_BACSU]] Reduces glyoxal and methylglyoxal. Is not involved in the vitamin B6 biosynthesis.
+
<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_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='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='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.
 +
== 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/d3/3d3f_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=3d3f ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
==About this Structure==
+
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<ref>PMID:19585557</ref>
-
[[3d3f]] is a 2 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=3D3F OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<ref group="xtra">PMID:019585557</ref><references group="xtra"/><references/>
+
</div>
-
[[Category: Bacillus globigii migula 1900]]
+
<div class="pdbe-citations 3d3f" style="background-color:#fffaf0;"></div>
-
[[Category: Lei, J.]]
+
== References ==
-
[[Category: Su, X D.]]
+
<references/>
-
[[Category: Zhou, Y F.]]
+
__TOC__
-
[[Category: Aldo-keto reductase]]
+
</StructureSection>
-
[[Category: Oxidoreductase]]
+
[[Category: Bacillus subtilis]]
 +
[[Category: Large Structures]]
 +
[[Category: Lei J]]
 +
[[Category: Su XD]]
 +
[[Category: Zhou YF]]

Current revision

Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis

PDB ID 3d3f

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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