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New page: left|200px<br /><applet load="2udp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2udp, resolution 1.80Å" /> '''UDP-GALACTOSE 4-EPIM...
 
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[[Image:2udp.jpg|left|200px]]<br /><applet load="2udp" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2udp, resolution 1.80&Aring;" />
'''UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL'''<br />


==Overview==
==UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL==
UDP-galactose 4-epimerase from Escherichia coli catalyzes the, interconversion of UDP-glucose and UDP-galactose. In recent years, the, enzyme has been the subject of intensive investigation due in part to its, ability to facilitate nonstereospecific hydride transfer between beta-NADH, and a 4-keto hexopyranose intermediate. The first molecular model of the, epimerase from E. coli was solved to 2.5 A resolution with crystals grown, in the presence of a substrate analogue, UDP-phenol (Bauer AJ, Rayment I, Frey PA, Holden HM, 1992, Proteins Struct Funct Genet 12:372-381). There, were concerns at the time that the inhibitor did not adequately mimic the, sugar moiety of a true substrate. Here we describe the high-resolution, X-ray crystal structure of the ternary complex of UDP-galactose, 4-epimerase with NADH and UDP-phenol. The model was refined to 1.8 A, resolution with a final overall R-factor of 18.6%. This high-resolution, structural analysis demonstrates that the original concerns were unfounded, and that, in fact, UDP-phenol and UDP-glucose bind similarly. The, carboxamide groups of the dinucleotides, in both subunits, are displaced, significantly from the planes of the nicotinamide rings by hydrogen, bonding interactions with Ser 124 and Tyr 149. UDP-galactose 4-epimerase, belongs to a family of enzymes known as the short-chain dehydrogenases, which contain a characteristic Tyr-Lys couple thought to be important for, catalysis. The epimerase/NADH/UDP-phenol model presented here represents a, well-defined ternary complex for this family of proteins and, as such, provides important information regarding the possible role of the Tyr-Lys, couple in the reaction mechanism.
<StructureSection load='2udp' size='340' side='right'caption='[[2udp]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2udp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1udp 1udp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UDP FirstGlance]. <br>
2UDP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NA, NAD, UPP and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1UDP. Active as [http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2UDP 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]] 1.8&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UPP:PHENYL-URIDINE-5-DIPHOSPHATE'>UPP</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=2udp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2udp OCA], [https://pdbe.org/2udp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2udp RCSB], [https://www.ebi.ac.uk/pdbsum/2udp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2udp ProSAT]</span></td></tr>
High-resolution X-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol., Thoden JB, Frey PA, Holden HM, Protein Sci. 1996 Nov;5(11):2149-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8931134 8931134]
</table>
== Function ==
[https://www.uniprot.org/uniprot/GALE_ECOLI GALE_ECOLI]  
== 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/ud/2udp_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=2udp ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: UDP-glucose 4-epimerase]]
[[Category: Gulick AM]]
[[Category: Gulick, A.]]
[[Category: Holden HM]]
[[Category: Holden, H.M.]]
[[Category: Thoden JB]]
[[Category: Thoden, J.B.]]
[[Category: EDO]]
[[Category: NA]]
[[Category: NAD]]
[[Category: UPP]]
[[Category: epimerase]]
[[Category: galactose metabolism]]
[[Category: isomerase]]
[[Category: udp-galactose]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 14:07:10 2007''

Latest revision as of 09:24, 21 February 2024

UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL

2udp, resolution 1.80Å

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