1zem

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1zem" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zem, resolution 1.9&Aring;" /> '''Crystal Structure of ...)
Current revision (07:07, 23 August 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zem.gif|left|200px]]<br /><applet load="1zem" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1zem, resolution 1.9&Aring;" />
 
-
'''Crystal Structure of NAD+-Bound Xylitol Dehydrogenase'''<br />
 
-
==Overview==
+
==Crystal Structure of NAD+-Bound Xylitol Dehydrogenase==
-
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.
+
<StructureSection load='1zem' size='340' side='right'caption='[[1zem]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
<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>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q8GR61_GLUOY Q8GR61_GLUOY]
 +
== 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/ze/1zem_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=1zem ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
==About this Structure==
+
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>
-
1ZEM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gluconobacter_oxydans Gluconobacter oxydans] with MG and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZEM OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity., Ehrensberger AH, Elling RA, Wilson DK, Structure. 2006 Mar;14(3):567-75. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16531240 16531240]
+
</div>
-
[[Category: D-xylulose reductase]]
+
<div class="pdbe-citations 1zem" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Gluconobacter oxydans]]
[[Category: Gluconobacter oxydans]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Ehrensberger, A.H.]]
+
[[Category: Ehrensberger AH]]
-
[[Category: Elling, R.A.]]
+
[[Category: Elling RA]]
-
[[Category: Wilson, D.K.]]
+
[[Category: Wilson DK]]
-
[[Category: MG]]
+
-
[[Category: NAD]]
+
-
[[Category: dinucleotide-binding domain]]
+
-
[[Category: rossmann fold]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:50:41 2007''
+

Current revision

Crystal Structure of NAD+-Bound Xylitol Dehydrogenase

PDB ID 1zem

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/1zem"
Personal tools