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| | <StructureSection load='5zxl' size='340' side='right'caption='[[5zxl]], [[Resolution|resolution]] 2.79Å' scene=''> | | <StructureSection load='5zxl' size='340' side='right'caption='[[5zxl]], [[Resolution|resolution]] 2.79Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zxl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZXL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zxl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZXL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.794Å</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='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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxl OCA], [http://pdbe.org/5zxl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zxl RCSB], [http://www.ebi.ac.uk/pdbsum/5zxl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxl ProSAT]</span></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=5zxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxl OCA], [https://pdbe.org/5zxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zxl RCSB], [https://www.ebi.ac.uk/pdbsum/5zxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxl ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GLDA_ECOLI GLDA_ECOLI]] Catalyzes the NAD-dependent oxidation of glycerol to dihydroxyacetone (glycerone). Allows microorganisms to utilize glycerol as a source of carbon under anaerobic conditions. In E.coli, an important role of GldA is also likely to regulate the intracellular level of dihydroxyacetone by catalyzing the reverse reaction, i.e. the conversion of dihydroxyacetone into glycerol. Possesses a broad substrate specificity, since it is also able to oxidize 1,2-propanediol and to reduce glycolaldehyde, methylglyoxal and hydroxyacetone into ethylene glycol, lactaldehyde and 1,2-propanediol, respectively.<ref>PMID:18179582</ref> <ref>PMID:18632294</ref> <ref>PMID:40950</ref> <ref>PMID:8132480</ref> | + | [https://www.uniprot.org/uniprot/GLDA_ECOLI GLDA_ECOLI] Catalyzes the NAD-dependent oxidation of glycerol to dihydroxyacetone (glycerone). Allows microorganisms to utilize glycerol as a source of carbon under anaerobic conditions. In E.coli, an important role of GldA is also likely to regulate the intracellular level of dihydroxyacetone by catalyzing the reverse reaction, i.e. the conversion of dihydroxyacetone into glycerol. Possesses a broad substrate specificity, since it is also able to oxidize 1,2-propanediol and to reduce glycolaldehyde, methylglyoxal and hydroxyacetone into ethylene glycol, lactaldehyde and 1,2-propanediol, respectively.<ref>PMID:18179582</ref> <ref>PMID:18632294</ref> <ref>PMID:40950</ref> <ref>PMID:8132480</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Glycerol dehydrogenase]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lin, L]] | + | [[Category: Lin L]] |
| - | [[Category: Zhang, J]] | + | [[Category: Zhang J]] |
| - | [[Category: Catalytic]]
| + | |
| - | [[Category: Dehydrogenase]]
| + | |
| - | [[Category: Glycerol]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
GLDA_ECOLI Catalyzes the NAD-dependent oxidation of glycerol to dihydroxyacetone (glycerone). Allows microorganisms to utilize glycerol as a source of carbon under anaerobic conditions. In E.coli, an important role of GldA is also likely to regulate the intracellular level of dihydroxyacetone by catalyzing the reverse reaction, i.e. the conversion of dihydroxyacetone into glycerol. Possesses a broad substrate specificity, since it is also able to oxidize 1,2-propanediol and to reduce glycolaldehyde, methylglyoxal and hydroxyacetone into ethylene glycol, lactaldehyde and 1,2-propanediol, respectively.[1] [2] [3] [4]
Publication Abstract from PubMed
Escherichia coli (strain K-12, substrain MG1655) glycerol dehydrogenase (GldA) is required to catalyze the first step in fermentative glycerol metabolism. The protein was expressed and purified to homogeneity using a simple combination of heat-shock and chromatographic methods. The high yield of the protein ( approximately 250 mg per litre of culture) allows large-scale production for potential industrial applications. Purified GldA exhibited a homogeneous tetrameric state ( approximately 161 kDa) in solution and relatively high thermostability (Tm = 65.6 degrees C). Sitting-drop sparse-matrix screens were used for protein crystallization. An optimized condition with ammonium sulfate (2 M) provided crystals suitable for diffraction, and a binary structure containing glycerol in the active site was solved at 2.8 A resolution. Each GldA monomer consists of nine beta-strands, thirteen alpha-helices, two 310-helices and several loops organized into two domains, the N- and C-terminal domains; the active site is located in a deep cleft between the two domains. The N-terminal domain contains a classic Rossmann fold for NAD(+) binding. The O1 and O2 atoms of glycerol serve as ligands for the tetrahedrally coordinated Zn(2+) ion. The orientation of the glycerol within the active site is mainly stabilized by van der Waals and electrostatic interactions with the benzyl ring of Phe245. Computer modeling suggests that the glycerol molecule is sandwiched by the Zn(2+) and NAD(+) ions. Based on this, the mechanism for the relaxed substrate specificity of this enzyme is also discussed.
Structure of glycerol dehydrogenase (GldA) from Escherichia coli.,Zhang J, Nanjaraj Urs AN, Lin L, Zhou Y, Hu Y, Hua G, Gao Q, Yuchi Z, Zhang Y Acta Crystallogr F Struct Biol Commun. 2019 Mar 1;75(Pt 3):176-183. doi:, 10.1107/S2053230X19000037. Epub 2019 Feb 21. PMID:30839292[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Subedi KP, Kim I, Kim J, Min B, Park C. Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12. FEMS Microbiol Lett. 2008 Feb;279(2):180-7. doi:, 10.1111/j.1574-6968.2007.01032.x. Epub 2007 Dec 20. PMID:18179582 doi:http://dx.doi.org/10.1111/j.1574-6968.2007.01032.x
- ↑ Gonzalez R, Murarka A, Dharmadi Y, Yazdani SS. A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab Eng. 2008 Sep;10(5):234-45. Epub 2008 May 27. PMID:18632294 doi:http://dx.doi.org/S1096-7176(08)00020-7
- ↑ Tang CT, Ruch FE Jr, Lin CC. Purification and properties of a nicotinamide adenine dinucleotide-linked dehydrogenase that serves an Escherichia coli mutant for glycerol catabolism. J Bacteriol. 1979 Oct;140(1):182-7. PMID:40950
- ↑ Truniger V, Boos W. Mapping and cloning of gldA, the structural gene of the Escherichia coli glycerol dehydrogenase. J Bacteriol. 1994 Mar;176(6):1796-800. PMID:8132480
- ↑ Zhang J, Nanjaraj Urs AN, Lin L, Zhou Y, Hu Y, Hua G, Gao Q, Yuchi Z, Zhang Y. Structure of glycerol dehydrogenase (GldA) from Escherichia coli. Acta Crystallogr F Struct Biol Commun. 2019 Mar 1;75(Pt 3):176-183. doi:, 10.1107/S2053230X19000037. Epub 2019 Feb 21. PMID:30839292 doi:http://dx.doi.org/10.1107/S2053230X19000037
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