1k8c: Difference between revisions

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==Crystal structure of dimeric xylose reductase in complex with NADP(H)==
==Crystal structure of dimeric xylose reductase in complex with NADP(H)==
<StructureSection load='1k8c' size='340' side='right' caption='[[1k8c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='1k8c' size='340' side='right'caption='[[1k8c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1k8c]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_10573 Atcc 10573]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K8C FirstGlance]. <br>
<table><tr><td colspan='2'>[[1k8c]] 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=1K8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K8C FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2.1&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jez|1jez]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xylR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=45596 ATCC 10573])</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=1k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8c OCA], [https://pdbe.org/1k8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k8c RCSB], [https://www.ebi.ac.uk/pdbsum/1k8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k8c ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='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=1k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8c OCA], [http://pdbe.org/1k8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k8c RCSB], [http://www.ebi.ac.uk/pdbsum/1k8c PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/1k8c_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/1k8c_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 21: Line 20:
</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=1k8c ConSurf].
</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=1k8c ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Xylose reductase is a homodimeric oxidoreductase dependent on NADPH or NADH and belongs to the largely monomeric aldo-keto reductase superfamily of proteins. It catalyzes the first step in the assimilation of xylose, an aldose found to be a major constituent monosaccharide of renewable plant hemicellulosic material, into yeast metabolic pathways. It does this by reducing open chain xylose to xylitol, which is reoxidized to xylulose by xylitol dehydrogenase and metabolically integrated via the pentose phosphate pathway. No structure has yet been determined for a xylose reductase, a dimeric aldo-keto reductase or a family 2 aldo-keto reductase. The structures of the Candida tenuis xylose reductase apo- and holoenzyme, which crystallize in spacegroup C2 with different unit cells, have been determined to 2.2 A resolution and an R-factor of 17.9 and 20.8%, respectively. Residues responsible for mediating the novel dimeric interface include Asp-178, Arg-181, Lys-202, Phe-206, Trp-313, and Pro-319. Alignments with other superfamily members indicate that these interactions are conserved in other dimeric xylose reductases but not throughout the remainder of the oligomeric aldo-keto reductases, predicting alternate modes of oligomerization for other families. An arrangement of side chains in a catalytic triad shows that Tyr-52 has a conserved function as a general acid. The loop that folds over the NAD(P)H cosubstrate is disordered in the apo form but becomes ordered upon cosubstrate binding. A slow conformational isomerization of this loop probably accounts for the observed rate-limiting step involving release of cosubstrate. Xylose binding (K(m) = 87 mM) is mediated by interactions with a binding pocket that is more polar than a typical aldo-keto reductase. Modeling of xylose into the active site of the holoenzyme using ordered waters as a guide for sugar hydroxyls suggests a convincing mode of substrate binding.
The structure of apo and holo forms of xylose reductase, a dimeric aldo-keto reductase from Candida tenuis.,Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK Biochemistry. 2002 Jul 16;41(28):8785-95. PMID:12102621<ref>PMID:12102621</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1k8c" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aldehyde reductase]]
[[Category: Large Structures]]
[[Category: Atcc 10573]]
[[Category: Yamadazyma tenuis]]
[[Category: Kavanagh, K L]]
[[Category: Kavanagh KL]]
[[Category: Klimacek, M]]
[[Category: Klimacek M]]
[[Category: Nidetzky, B]]
[[Category: Nidetzky B]]
[[Category: Wilson, D K]]
[[Category: Wilson DK]]
[[Category: Aldo-keto reductase]]
[[Category: Beta-alpha barrel]]
[[Category: Oxidoreductase]]

Latest revision as of 10:44, 7 February 2024

Crystal structure of dimeric xylose reductase in complex with NADP(H)Crystal structure of dimeric xylose reductase in complex with NADP(H)

Structural highlights

1k8c is a 4 chain structure with sequence from Yamadazyma tenuis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYL1_CANTE Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1k8c, resolution 2.10Å

Drag the structure with the mouse to rotate

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