1r66

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[[Image:1r66.jpg|left|200px]]
 
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{{Structure
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==Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound==
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|PDB= 1r66 |SIZE=350|CAPTION= <scene name='initialview01'>1r66</scene>, resolution 1.44&Aring;
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<StructureSection load='1r66' size='340' side='right'caption='[[1r66]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> and <scene name='pdbligand=TYD:THYMIDINE-5&#39;- DIPHOSPHATE'>TYD</scene>
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<table><tr><td colspan='2'>[[1r66]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R66 FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46]
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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]] 1.44&#8491;</td></tr>
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|GENE= DesIV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
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}}
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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=1r66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r66 OCA], [https://pdbe.org/1r66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r66 RCSB], [https://www.ebi.ac.uk/pdbsum/1r66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r66 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9ZGH3_STRVZ Q9ZGH3_STRVZ]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r6/1r66_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1r66 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in some macrolide antibiotics. In Streptomyces venezuelae, there are seven genes required for the biosynthesis of this unusual sugar. One of the genes, desIV, codes for a dTDP-glucose 4,6-dehydratase, which is referred to as DesIV. The reaction mechanisms for these types of dehydratases are quite complicated with proton abstraction from the sugar 4'-hydroxyl group and hydride transfer to NAD+, proton abstraction at C-5, and elimination of the hydroxyl group at C-6 of the sugar, and finally return of a proton to C-5 and a hydride from NADH to C-6. Here we describe the cloning, overexpression, and purification, and high resolution x-ray crystallographic analysis to 1.44 A of wild-type DesIV complexed with dTDP. Additionally, for this study, a double site-directed mutant protein (D128N/E129Q) was prepared, crystallized as a complex with NAD+ and the substrate dTDP-glucose and its structure determined to 1.35 A resolution. In DesIV, the phenolate group of Tyr(151) and O(gamma) of Thr(127) lie at 2.7 and 2.6 A, respectively from the 4'-hydroxyl group of the dTDP-glucose substrate. The side chain of Asp(128) is in the correct position to function as a general acid for proton donation to the 6'-hydroxyl group while the side chain of Glu(129) is ideally situated to serve as the general base for proton abstraction at C-5. This investigation provides further detailed information for understanding the exquisite chemistry that occurs in these remarkable enzymes.
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'''Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound'''
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High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae.,Allard ST, Cleland WW, Holden HM J Biol Chem. 2004 Jan 16;279(3):2211-20. Epub 2003 Oct 21. PMID:14570895<ref>PMID:14570895</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1r66" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in some macrolide antibiotics. In Streptomyces venezuelae, there are seven genes required for the biosynthesis of this unusual sugar. One of the genes, desIV, codes for a dTDP-glucose 4,6-dehydratase, which is referred to as DesIV. The reaction mechanisms for these types of dehydratases are quite complicated with proton abstraction from the sugar 4'-hydroxyl group and hydride transfer to NAD+, proton abstraction at C-5, and elimination of the hydroxyl group at C-6 of the sugar, and finally return of a proton to C-5 and a hydride from NADH to C-6. Here we describe the cloning, overexpression, and purification, and high resolution x-ray crystallographic analysis to 1.44 A of wild-type DesIV complexed with dTDP. Additionally, for this study, a double site-directed mutant protein (D128N/E129Q) was prepared, crystallized as a complex with NAD+ and the substrate dTDP-glucose and its structure determined to 1.35 A resolution. In DesIV, the phenolate group of Tyr(151) and O(gamma) of Thr(127) lie at 2.7 and 2.6 A, respectively from the 4'-hydroxyl group of the dTDP-glucose substrate. The side chain of Asp(128) is in the correct position to function as a general acid for proton donation to the 6'-hydroxyl group while the side chain of Glu(129) is ideally situated to serve as the general base for proton abstraction at C-5. This investigation provides further detailed information for understanding the exquisite chemistry that occurs in these remarkable enzymes.
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*[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]]
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== References ==
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==About this Structure==
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<references/>
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1R66 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R66 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae., Allard ST, Cleland WW, Holden HM, J Biol Chem. 2004 Jan 16;279(3):2211-20. Epub 2003 Oct 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14570895 14570895]
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[[Category: Single protein]]
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[[Category: Streptomyces venezuelae]]
[[Category: Streptomyces venezuelae]]
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[[Category: dTDP-glucose 4,6-dehydratase]]
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[[Category: Allard STM]]
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[[Category: Allard, S T.M.]]
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[[Category: Cleland WW]]
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[[Category: Cleland, W W.]]
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[[Category: Holden HM]]
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[[Category: Holden, H M.]]
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[[Category: CL]]
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[[Category: NAD]]
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[[Category: TYD]]
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[[Category: dehydratase]]
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[[Category: rossmann fold]]
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[[Category: short-chain dehydrogenase/reductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:26:07 2008''
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Current revision

Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound

PDB ID 1r66

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