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1jpu

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(New page: 200px<br /><applet load="1jpu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jpu, resolution 1.80&Aring;" /> '''Crystal Structure of...)
Current revision (07:41, 7 February 2024) (edit) (undo)
 
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[[Image:1jpu.jpg|left|200px]]<br /><applet load="1jpu" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1jpu, resolution 1.80&Aring;" />
 
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'''Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase'''<br />
 
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==Overview==
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==Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase==
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BACKGROUND: Bacillus stearothermophilus glycerol dehydrogenase (GlyDH), (glycerol:NAD(+) 2-oxidoreductase, EC 1.1.1.6) catalyzes the oxidation of, glycerol to dihydroxyacetone (1,3-dihydroxypropanone) with concomitant, reduction of NAD(+) to NADH. Analysis of the sequence of this enzyme, indicates that it is a member of the so-called iron-containing alcohol, dehydrogenase family. Despite this sequence similarity, GlyDH shows a, strict dependence on zinc for activity. On the basis of this, we propose, to rename this group the family III metal-dependent polyol dehydrogenases., To date, no structural data have been reported for any enzyme in this, group. RESULTS: The crystal structure of B. stearothermophilus glycerol, dehydrogenase has been determined at 1.7 A resolution to provide, structural insights into the mechanistic features of this family. The, enzyme has 370 amino acid residues, has a molecular mass of 39.5 kDa, and, is a homooctamer in solution. CONCLUSIONS: Analysis of the crystal, structures of the free enzyme and of the binary complexes with NAD(+) and, glycerol show that the active site of GlyDH lies in the cleft between the, enzyme's two domains, with the catalytic zinc ion playing a role in, stabilizing an alkoxide intermediate. In addition, the specificity of this, enzyme for a range of diols can be understood, as both hydroxyls of the, glycerol form ligands to the enzyme-bound Zn(2+) ion at the active site., The structure further reveals a previously unsuspected similarity to, dehydroquinate synthase, an enzyme whose more complex chemistry shares a, common chemical step with that catalyzed by glycerol dehydrogenase, providing a striking example of divergent evolution. Finally, the, structure suggests that the NAD(+) binding domain of GlyDH may be related, to that of the classical Rossmann fold by switching the sequence order of, the two mononucleotide binding folds that make up this domain.
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<StructureSection load='1jpu' size='340' side='right'caption='[[1jpu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1jpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JPU FirstGlance]. <br>
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1JPU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycerol_dehydrogenase Glycerol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.6 1.1.1.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JPU OCA].
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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=ZN:ZINC+ION'>ZN</scene></td></tr>
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==Reference==
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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=1jpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpu OCA], [https://pdbe.org/1jpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jpu RCSB], [https://www.ebi.ac.uk/pdbsum/1jpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jpu ProSAT]</span></td></tr>
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Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase., Ruzheinikov SN, Burke J, Sedelnikova S, Baker PJ, Taylor R, Bullough PA, Muir NM, Gore MG, Rice DW, Structure. 2001 Sep;9(9):789-802. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11566129 11566129]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GLDA_GEOSE GLDA_GEOSE] Catalyzes the NAD-dependent oxidation of glycerol to dihydroxyacetone (glycerone). Allows microorganisms to utilize glycerol as a source of carbon under anaerobic conditions. Is also able to use various diols as substrates, such as propan-1,2-diol, butan-2,3-diol, ethan-1,2-diol, and 3-mercapto-1,2-dihydroxypropane.<ref>PMID:2493267</ref>
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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/jp/1jpu_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=1jpu ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
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[[Category: Glycerol dehydrogenase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Baker PJ]]
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[[Category: Baker, P.J.]]
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[[Category: Bullough PA]]
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[[Category: Bullough, P.A.]]
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[[Category: Burke J]]
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[[Category: Burke, J.]]
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[[Category: Gore MG]]
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[[Category: Gore, M.G.]]
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[[Category: Muir NM]]
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[[Category: Muir, N.M.]]
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[[Category: Rice DW]]
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[[Category: Rice, D.W.]]
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[[Category: Ruzheinikov SN]]
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[[Category: Ruzheinikov, S.N.]]
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[[Category: Sedelnikova S]]
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[[Category: Sedelnikova, S.]]
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[[Category: Taylor R]]
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[[Category: Taylor, R.]]
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[[Category: ZN]]
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[[Category: glycerol metabolism]]
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[[Category: nad]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:27:51 2007''
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Current revision

Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase

PDB ID 1jpu

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