|
|
| Line 3: |
Line 3: |
| | <StructureSection load='1dxy' size='340' side='right'caption='[[1dxy]], [[Resolution|resolution]] 1.86Å' scene=''> | | <StructureSection load='1dxy' size='340' side='right'caption='[[1dxy]], [[Resolution|resolution]] 1.86Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1dxy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1DXY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1dxy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DXY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COI:2-OXO-4-METHYLPENTANOIC+ACID'>COI</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.86Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COI:2-OXO-4-METHYLPENTANOIC+ACID'>COI</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1dxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dxy OCA], [http://pdbe.org/1dxy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dxy RCSB], [http://www.ebi.ac.uk/pdbsum/1dxy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dxy 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=1dxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dxy OCA], [https://pdbe.org/1dxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dxy RCSB], [https://www.ebi.ac.uk/pdbsum/1dxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dxy ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DHD2_LACPA DHD2_LACPA]] Catalyzes the NAD dependent reversible, stereospecific interconversion between 2-ketocarboxylic acids and D-2-hydroxy-carboxylic acids. | + | [https://www.uniprot.org/uniprot/DHD2_LACPA DHD2_LACPA] Catalyzes the NAD dependent reversible, stereospecific interconversion between 2-ketocarboxylic acids and D-2-hydroxy-carboxylic acids. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 33: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus a von freudenreich 1890]] | + | [[Category: Lacticaseibacillus casei]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dengler, U]] | + | [[Category: Dengler U]] |
| - | [[Category: Kiess, M]] | + | [[Category: Kiess M]] |
| - | [[Category: Niefind, K]] | + | [[Category: Niefind K]] |
| - | [[Category: Schomburg, D]] | + | [[Category: Schomburg D]] |
| - | [[Category: D-2-hydroxycarboxylate dehydrogenase]]
| + | |
| - | [[Category: D-lactate dehydrogenase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
DHD2_LACPA Catalyzes the NAD dependent reversible, stereospecific interconversion between 2-ketocarboxylic acids and D-2-hydroxy-carboxylic acids.
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
D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei is a homodimer with 333 amino acids and a molecular mass of 37 kDa per subunit. The enzyme belongs to the protein family of NAD+-dependent D-2-hydroxycarboxylate dehydrogenases and within this family to the subgroup of D-lactate dehydrogenases (D-LDHs). Compared with other D-LDHs D-HicDH is characterized by a very low specificity regarding size and chemical constitution of the accepted D-2-hydroxycarboxylates. Hexagonal crystals of recombinant D-HicDH in the presence of NAD+ and 2-oxoisocaproate (4-methyl-2-oxopentanoate) were grown with ammonium sulphate as precipitating agent. The structure of these crystals was solved by molecular replacement and refined to a final R-factor of 19.6% for all measured X-ray reflections in the resolution range (infinity to 1.86 A). Both NAD+ and 2-oxoisocaproate were identified in the electron density map; binding of the latter in the active site, however, competes with a sulphate ion, which is also defined by electron density. Additionally the final model contains 182 water molecules and a second sulphate ion. The binding of both an in vitro substrate and the natural cosubstrate in the active site provides substantial insight into the catalytic mechanism and allows us to assess previously published active site models for this enzyme family, in particular the two most controversial points, the role of the conserved Arg234 and substrate binding. Furthermore the overall topology and details of the D-HicDH structure are described, discussed against the background of homologous structures and compared with one closely and one distantly related protein.
Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution.,Dengler U, Niefind K, Kiess M, Schomburg D J Mol Biol. 1997 Apr 4;267(3):640-60. PMID:9126843[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dengler U, Niefind K, Kiess M, Schomburg D. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. J Mol Biol. 1997 Apr 4;267(3):640-60. PMID:9126843
|
