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| | ==L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis== | | ==L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis== |
| - | <StructureSection load='3gfb' size='340' side='right' caption='[[3gfb]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='3gfb' size='340' side='right'caption='[[3gfb]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gfb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GFB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3gfb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GFB 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=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]] 2.4Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tdh, TK0916 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-threonine_3-dehydrogenase L-threonine 3-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.103 1.1.1.103] </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=3gfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfb OCA], [https://pdbe.org/3gfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gfb RCSB], [https://www.ebi.ac.uk/pdbsum/3gfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfb ProSAT]</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=3gfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfb OCA], [http://pdbe.org/3gfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gfb RCSB], [http://www.ebi.ac.uk/pdbsum/3gfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TDH_THEKO TDH_THEKO] |
| | == 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/gf/3gfb_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gf/3gfb_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: L-threonine 3-dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bowyer, A]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Metal-binding]] | + | [[Category: Bowyer A]] |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
TDH_THEKO
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
The X-ray structure of the holo-form of l-threonine dehydrogenase (TDH) from Thermococcus kodakaraensis (TkTDH) has been determined at 2.4A resolution. TDH catalyses the NAD(+)-dependent oxidation of l-threonine to 2-amino-3-ketobutyrate, and is one of the first enzymes in this family to be solved by X-ray crystallography. The enzyme is a homo-tetramer, each monomer consisting of 350 amino acids that form two domains; a catalytic domain and a nicotinamide co-factor (NAD(+))-binding domain, which contains an alpha/beta Rossmann fold motif. An extended twelve-stranded beta-sheet is formed by the association of pairs of monomers in the tetramer. TkTDH shows strong overall structural similarity to TDHs from thermophiles and alcohol dehydrogenases (ADH) from lower life forms, despite low sequence homology, exhibiting the same overall fold of the monomer and assembly of the tetramer. The structure reveals the binding site of the essential co-factor NAD(+) which is present in all subunits. Docking studies suggest a mode of interaction of TDH with 2-amino-3-ketobutyrate CoA ligase, the subsequent enzyme in the pathway for conversion of threonine to glycine. TDH is known to form a stable functional complex with 2-amino-3-ketobutyrate ligase, most probably to shield an unstable intermediate.
Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis.,Bowyer A, Mikolajek H, Stuart JW, Wood SP, Jamil F, Rashid N, Akhtar M, Cooper JB J Struct Biol. 2009 Nov;168(2):294-304. Epub 2009 Jul 16. PMID:19616102[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bowyer A, Mikolajek H, Stuart JW, Wood SP, Jamil F, Rashid N, Akhtar M, Cooper JB. Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Struct Biol. 2009 Nov;168(2):294-304. Epub 2009 Jul 16. PMID:19616102 doi:10.1016/j.jsb.2009.07.011
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