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New page: left|200px<br /><applet load="1orr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1orr, resolution 1.50Å" /> '''Crystal Structure of...
 
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[[Image:1orr.jpg|left|200px]]<br /><applet load="1orr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1orr, resolution 1.50&Aring;" />
'''Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP'''<br />


==Overview==
==Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP==
Tyvelose epimerase catalyzes the last step in the biosynthesis of tyvelose, by converting CDP-d-paratose to CDP-d-tyvelose. This unusual, 3,6-dideoxyhexose occurs in the O-antigens of some types of Gram-negative, bacteria. Here we describe the cloning, protein purification, and, high-resolution x-ray crystallographic analysis of tyvelose epimerase from, Salmonella typhi complexed with CDP. The enzyme from S. typhi is a, homotetramer with each subunit containing 339 amino acid residues and a, tightly bound NAD+ cofactor. The quaternary structure of the enzyme, displays 222 symmetry and can be aptly described as a dimer of dimers., Each subunit folds into two distinct lobes: the N-terminal motif, responsible for NAD+ binding and the C-terminal region that harbors the, binding site for CDP. The analysis described here demonstrates that, tyvelose epimerase belongs to the short-chain dehydrogenase/reductase, superfamily of enzymes. Indeed, its active site is reminiscent to that, observed for UDP-galactose 4-epimerase, an enzyme that plays a key role in, galactose metabolism. Unlike UDP-galactose 4-epimerase where the, conversion of configuration occurs about C-4 of the UDP-glucose or, UDP-galactose substrates, in the reaction catalyzed by tyvelose epimerase, the inversion of stereochemistry occurs at C-2. On the basis of the, observed binding mode for CDP, it is possible to predict the manner in, which the substrate, CDP-paratose, and the product, CDP-tyvelose, might be, accommodated within the active site of tyvelose epimerase.
<StructureSection load='1orr' size='340' side='right'caption='[[1orr]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1orr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhi Salmonella enterica subsp. enterica serovar Typhi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ORR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ORR FirstGlance]. <br>
1ORR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhi Salmonella typhi] with NAD and CDP as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ORR 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]] 1.5&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1orr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1orr OCA], [https://pdbe.org/1orr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1orr RCSB], [https://www.ebi.ac.uk/pdbsum/1orr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1orr ProSAT]</span></td></tr>
High resolution x-ray structure of tyvelose epimerase from Salmonella typhi., Koropatkin NM, Liu HW, Holden HM, J Biol Chem. 2003 Jun 6;278(23):20874-81. Epub 2003 Mar 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12642575 12642575]
</table>
[[Category: Salmonella typhi]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/RFBE_SALTI RFBE_SALTI] Catalyzes the isomeration of CDP-paratose to CDP-tyvelose.
[[Category: Holden, H.M.]]
== Evolutionary Conservation ==
[[Category: Koropatkin, N.M.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Liu, H.]]
Check<jmol>
[[Category: CDP]]
  <jmolCheckbox>
[[Category: NAD]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/or/1orr_consurf.spt"</scriptWhenChecked>
[[Category: rossmann fold]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: short-chain dehydrogenase/reductase]]
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:08:10 2007''
</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=1orr ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Salmonella enterica subsp. enterica serovar Typhi]]
[[Category: Holden HM]]
[[Category: Koropatkin NM]]
[[Category: Liu H]]

Latest revision as of 08:02, 14 February 2024

Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP

1orr, resolution 1.50Å

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