1k8c: Difference between revisions

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New page: left|200px<br /><applet load="1k8c" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k8c, resolution 2.10Å" /> '''Crystal structure of...
 
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[[Image:1k8c.jpg|left|200px]]<br /><applet load="1k8c" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1k8c, resolution 2.10&Aring;" />
'''Crystal structure of dimeric xylose reductase in complex with NADP(H)'''<br />


==Overview==
==Crystal structure of dimeric xylose reductase in complex with NADP(H)==
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.
<StructureSection load='1k8c' size='340' side='right'caption='[[1k8c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
1K8C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Candida_tenuis Candida tenuis] with NAP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K8C OCA].  
</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='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>
==Reference==
<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>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12102621 12102621]
</table>
[[Category: Aldehyde reductase]]
== Function ==
[[Category: Candida tenuis]]
[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.
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Kavanagh, K.L.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Klimacek, M.]]
Check<jmol>
[[Category: Nidetzky, B.]]
  <jmolCheckbox>
[[Category: Wilson, D.K.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/1k8c_consurf.spt"</scriptWhenChecked>
[[Category: NAP]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: aldo-keto reductase]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: beta-alpha barrel]]
  </jmolCheckbox>
[[Category: nadp(h)]]
</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>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:56:58 2007''
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Yamadazyma tenuis]]
[[Category: Kavanagh KL]]
[[Category: Klimacek M]]
[[Category: Nidetzky B]]
[[Category: Wilson DK]]

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

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