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| | ==Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+== | | ==Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+== |
| - | <StructureSection load='1jq5' size='340' side='right' caption='[[1jq5]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='1jq5' size='340' side='right'caption='[[1jq5]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1jq5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQ5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1jq5]] 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=1JQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQ5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jqa|1jqa]], [[1jpu|1jpu]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GLDA or GLD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=1jq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jq5 OCA], [https://pdbe.org/1jq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jq5 RCSB], [https://www.ebi.ac.uk/pdbsum/1jq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jq5 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jq5 OCA], [http://pdbe.org/1jq5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jq5 RCSB], [http://www.ebi.ac.uk/pdbsum/1jq5 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jq/1jq5_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jq/1jq5_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Glycerol dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Baker, P J]] | + | [[Category: Baker PJ]] |
| - | [[Category: Bullough, P A]] | + | [[Category: Bullough PA]] |
| - | [[Category: Burke, J]] | + | [[Category: Burke J]] |
| - | [[Category: Gore, M G]] | + | [[Category: Gore MG]] |
| - | [[Category: Muir, N M]] | + | [[Category: Muir NM]] |
| - | [[Category: Rice, D W]] | + | [[Category: Rice DW]] |
| - | [[Category: Ruzheinikov, S N]] | + | [[Category: Ruzheinikov SN]] |
| - | [[Category: Sedelnikova, S]] | + | [[Category: Sedelnikova S]] |
| - | [[Category: Taylor, R]] | + | [[Category: Taylor R]] |
| - | [[Category: Glycerol metabolism]]
| + | |
| - | [[Category: Nad]]
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| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
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.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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:11566129[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Spencer P, Bown KJ, Scawen MD, Atkinson T, Gore MG. Isolation and characterisation of the glycerol dehydrogenase from Bacillus stearothermophilus. Biochim Biophys Acta. 1989 Feb 23;994(3):270-9. PMID:2493267
- ↑ Ruzheinikov SN, Burke J, Sedelnikova S, Baker PJ, Taylor R, Bullough PA, Muir NM, Gore MG, Rice DW. Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase. Structure. 2001 Sep;9(9):789-802. PMID:11566129
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