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| | <StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution|resolution]] 1.52Å' scene=''> | | <StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution|resolution]] 1.52Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_fragi"_eichholz_1902 "bacterium fragi" eichholz 1902]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1T FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.52Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wmb|1wmb]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [https://pdbe.org/1x1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [https://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t 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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [https://pdbe.org/1x1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [https://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5KST5_PSEFR Q5KST5_PSEFR] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium fragi eichholz 1902]] | |
| - | [[Category: 3-hydroxybutyrate dehydrogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ichihara, E]] | + | [[Category: Pseudomonas fragi]] |
| - | [[Category: Ito, K]] | + | [[Category: Ichihara E]] |
| - | [[Category: Nakajima, Y]] | + | [[Category: Ito K]] |
| - | [[Category: Ogawa, K]] | + | [[Category: Nakajima Y]] |
| - | [[Category: Yoshimoto, T]] | + | [[Category: Ogawa K]] |
| - | [[Category: Beta-hydroxybutyrate]]
| + | [[Category: Yoshimoto T]] |
| - | [[Category: Ketone body]]
| + | |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Nadh]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Sdr]]
| + | |
| - | [[Category: Short chain dehydrogenase]]
| + | |
| Structural highlights
Function
Q5KST5_PSEFR
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 gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open reading frame encoding a 260 amino acid residue protein. The recombinant enzyme was efficiently expressed in Escherichia coli cells harboring pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme showed a strict stereospecificity to the D-enantiomer (3R-configuration) of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by the multiwavelength anomalous diffraction method using the SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate anion was observed in both the ligand-free enzyme and the enzyme-NAD+ complex, and was located near the catalytic tetrad. It was shown that the cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate dehydrogenation competitively, with a Ki value of 5.6 mM. From the interactions between cacodylate and the enzyme, it is predicted that substrate specificity is achieved through the recognition of the 3-methyl and carboxyl groups of the substrate.
D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme.,Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:16325199[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T. D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme. J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:16325199 doi:10.1016/j.jmb.2005.10.072
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