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2udp

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[[Image:2udp.jpg|left|200px]]
 
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==UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL==
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The line below this paragraph, containing "STRUCTURE_2udp", creates the "Structure Box" on the page.
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<StructureSection load='2udp' size='340' side='right'caption='[[2udp]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_2udp| PDB=2udp | SCENE= }}
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<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>
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</table>
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'''UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL'''
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== Function ==
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[https://www.uniprot.org/uniprot/GALE_ECOLI GALE_ECOLI]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ud/2udp_consurf.spt"</scriptWhenChecked>
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2UDP is a [[Single protein]] structure of sequence from [http://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].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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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://www.ncbi.nlm.nih.gov/pubmed/8931134 8931134]
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</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].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: UDP-glucose 4-epimerase]]
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[[Category: Gulick AM]]
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[[Category: Gulick, A.]]
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[[Category: Holden HM]]
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[[Category: Holden, H M.]]
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[[Category: Thoden JB]]
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[[Category: Thoden, J B.]]
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[[Category: Epimerase]]
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[[Category: Galactose metabolism]]
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[[Category: Isomerase]]
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[[Category: Udp-galactose]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 17:28:20 2008''
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Current revision

UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL

PDB ID 2udp

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