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1zem

From Proteopedia

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[[Image:1zem.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of NAD+-Bound Xylitol Dehydrogenase==
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|PDB= 1zem |SIZE=350|CAPTION= <scene name='initialview01'>1zem</scene>, resolution 1.9&Aring;
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<StructureSection load='1zem' size='340' side='right'caption='[[1zem]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
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<table><tr><td colspan='2'>[[1zem]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Gluconobacter_oxydans Gluconobacter oxydans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZEM FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylulose_reductase D-xylulose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.9 1.1.1.9] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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|GENE= AB091690 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=442 Gluconobacter oxydans])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zem OCA], [https://pdbe.org/1zem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zem RCSB], [https://www.ebi.ac.uk/pdbsum/1zem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zem ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zem OCA], [http://www.ebi.ac.uk/pdbsum/1zem PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zem RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/Q8GR61_GLUOY Q8GR61_GLUOY]
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== Evolutionary Conservation ==
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'''Crystal Structure of NAD+-Bound Xylitol Dehydrogenase'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ze/1zem_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1zem ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Xylitol dehydrogenase (XDH) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. For efficient xylose utilization at high flux rates, cosubstrates should be recycled between the NAD+-specific XDH and the NADPH-preferring xylose reductase, another enzyme in the pathway. To understand and alter the cosubstrate specificity of XDH, we determined the crystal structure of the Gluconobacter oxydans holoenzyme to 1.9 angstroms resolution. The structure reveals that NAD+ specificity is largely conferred by Asp38, which interacts with the hydroxyls of the adenosine ribose. Met39 stacked under the purine ring and was also located near the 2' hydroxyl. Based on the location of these residues and on sequence alignments with related enzymes of various cosubstrate specificities, we constructed a double mutant (D38S/M39R) that was able to exclusively use NADP+, with no loss of activity.
Xylitol dehydrogenase (XDH) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. For efficient xylose utilization at high flux rates, cosubstrates should be recycled between the NAD+-specific XDH and the NADPH-preferring xylose reductase, another enzyme in the pathway. To understand and alter the cosubstrate specificity of XDH, we determined the crystal structure of the Gluconobacter oxydans holoenzyme to 1.9 angstroms resolution. The structure reveals that NAD+ specificity is largely conferred by Asp38, which interacts with the hydroxyls of the adenosine ribose. Met39 stacked under the purine ring and was also located near the 2' hydroxyl. Based on the location of these residues and on sequence alignments with related enzymes of various cosubstrate specificities, we constructed a double mutant (D38S/M39R) that was able to exclusively use NADP+, with no loss of activity.
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==About this Structure==
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Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity.,Ehrensberger AH, Elling RA, Wilson DK Structure. 2006 Mar;14(3):567-75. PMID:16531240<ref>PMID:16531240</ref>
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1ZEM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gluconobacter_oxydans Gluconobacter oxydans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZEM OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity., Ehrensberger AH, Elling RA, Wilson DK, Structure. 2006 Mar;14(3):567-75. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16531240 16531240]
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</div>
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[[Category: D-xylulose reductase]]
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<div class="pdbe-citations 1zem" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Gluconobacter oxydans]]
[[Category: Gluconobacter oxydans]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ehrensberger, A H.]]
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[[Category: Ehrensberger AH]]
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[[Category: Elling, R A.]]
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[[Category: Elling RA]]
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[[Category: Wilson, D K.]]
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[[Category: Wilson DK]]
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[[Category: dinucleotide-binding domain]]
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[[Category: rossmann fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:34:57 2008''
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Current revision

Crystal Structure of NAD+-Bound Xylitol Dehydrogenase

PDB ID 1zem

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