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| - | [[Image:1mi3.gif|left|200px]] | |
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| - | {{Structure
| + | ==1.8 Angstrom structure of xylose reductase from Candida tenuis in complex with NAD== |
| - | |PDB= 1mi3 |SIZE=350|CAPTION= <scene name='initialview01'>1mi3</scene>, resolution 1.80Å
| + | <StructureSection load='1mi3' size='340' side='right'caption='[[1mi3]], [[Resolution|resolution]] 1.80Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
| + | <table><tr><td colspan='2'>[[1mi3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yamadazyma_tenuis Yamadazyma tenuis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MI3 FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_reductase Aldehyde reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.21 1.1.1.21] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | |GENE= xylR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=45596 Candida tenuis])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi3 OCA], [https://pdbe.org/1mi3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mi3 RCSB], [https://www.ebi.ac.uk/pdbsum/1mi3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi3 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1jez|1JEZ]], [[1k8c|1K8C]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi3 OCA], [http://www.ebi.ac.uk/pdbsum/1mi3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1mi3 RCSB]</span> | + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/XYL1_CANTE XYL1_CANTE] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate. |
| - | | + | == Evolutionary Conservation == |
| - | '''1.8 Angstrom structure of xylose reductase from Candida tenuis in complex with NADH'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mi/1mi3_consurf.spt"</scriptWhenChecked> |
| - | The co-ordinates reported have been submitted to the Protein Data Bank under accession number 1MI3. Xylose reductase (XR; AKR2B5) is an unusual member of aldo-keto reductase superfamily, because it is one of the few able to efficiently utilize both NADPH and NADH as co-substrates in converting xylose into xylitol. In order to better understand the basis for this dual specificity, we have determined the crystal structure of XR from the yeast Candida tenuis in complex with NAD(+) to 1.80 A resolution (where 1 A=0.1 nm) with a crystallographic R -factor of 18.3%. A comparison of the NAD(+)- and the previously determined NADP(+)-bound forms of XR reveals that XR has the ability to change the conformation of two loops. To accommodate both the presence and absence of the 2'-phosphate, the enzyme is able to adopt different conformations for several different side chains on these loops, including Asn(276), which makes alternative hydrogen-bonding interactions with the adenosine ribose. Also critical is the presence of Glu(227) on a short rigid helix, which makes hydrogen bonds to both the 2'- and 3'-hydroxy groups of the adenosine ribose. In addition to changes in hydrogen-bonding of the adenosine, the ribose unmistakably adopts a 3'- endo conformation rather than the 2'- endo conformation seen in the NADP(+)-bound form. These results underscore the importance of tight adenosine binding for efficient use of either NADH or NADPH as a co-substrate in aldo-keto reductases. The dual specificity found in XR is also an important consideration in designing a high-flux xylose metabolic pathway, which may be improved with an enzyme specific for NADH.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1MI3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Candida_tenuis Candida tenuis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI3 OCA].
| + | </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=1mi3 ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference==
| + | __TOC__ |
| - | Structure of xylose reductase bound to NAD+ and the basis for single and dual co-substrate specificity in family 2 aldo-keto reductases., Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK, Biochem J. 2003 Jul 15;373(Pt 2):319-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12733986 12733986]
| + | </StructureSection> |
| - | [[Category: Aldehyde reductase]]
| + | [[Category: Large Structures]] |
| - | [[Category: Candida tenuis]] | + | [[Category: Yamadazyma tenuis]] |
| - | [[Category: Single protein]] | + | [[Category: Kavanagh KL]] |
| - | [[Category: Kavanagh, K L.]] | + | [[Category: Klimacek M]] |
| - | [[Category: Klimacek, M.]] | + | [[Category: Nidetzky B]] |
| - | [[Category: Nidetzky, B.]] | + | [[Category: Wilson DK]] |
| - | [[Category: Wilson, D K.]] | + | |
| - | [[Category: aldo-keto reductase]]
| + | |
| - | [[Category: beta-alpha barrel]]
| + | |
| - | [[Category: dimer]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:16:18 2008''
| + | |
