1jpu: Difference between revisions

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-[[Image:1jpu.jpg|left|200px]]
- {{Structure
+==Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase==
-|PDB= 1jpu |SIZE=350|CAPTION= <scene name='initialview01'>1jpu</scene>, resolution 1.80&Aring;
+<StructureSection load='1jpu' size='340' side='right'caption='[[1jpu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
+<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>
-|ACTIVITY= [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]
+</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>
-|GENE= GLDA or GLD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])
+<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>
-}}
+<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>
+</table>
-'''Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase'''
+== Function ==
+[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>
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-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.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/1jpu_consurf.spt"</scriptWhenChecked>
-JPU is a [[Single protein]] structure of sequence from [http://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].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-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://www.ncbi.nlm.nih.gov/pubmed/11566129 11566129]
+</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].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Glycerol dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Baker PJ]]
-[[Category: Baker, P J.]]
+[[Category: Bullough PA]]
-[[Category: Bullough, P A.]]
+[[Category: Burke J]]
-[[Category: Burke, J.]]
+[[Category: Gore MG]]
-[[Category: Gore, M G.]]
+[[Category: Muir NM]]
-[[Category: Muir, N M.]]
+[[Category: Rice DW]]
-[[Category: Rice, D W.]]
+[[Category: Ruzheinikov SN]]
-[[Category: Ruzheinikov, S N.]]
+[[Category: Sedelnikova S]]
-[[Category: Sedelnikova, S.]]
+[[Category: Taylor R]]
-[[Category: Taylor, R.]]
-[[Category: ZN]]
-[[Category: glycerol metabolism]]
-[[Category: nad]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:06:47 2008''