5XTG
Crystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1 in the presence of NAD+ and 2,3-dihydroxybiphenyl
Summary for 5XTG
| Entry DOI | 10.2210/pdb5xtg/pdb |
| Descriptor | 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, CITRIC ACID, ... (5 entities in total) |
| Functional Keywords | tetramer, cis-dihydrodiol naphthalene dehydrogenase, oxidoreductase |
| Biological source | Pseudomonas sp. MC1 |
| Total number of polymer chains | 1 |
| Total formula weight | 30862.99 |
| Authors | Park, A.K.,Kim, H.-W. (deposition date: 2017-06-19, release date: 2017-08-09, Last modification date: 2023-11-22) |
| Primary citation | Park, A.K.,Kim, H.,Kim, I.S.,Roh, S.J.,Shin, S.C.,Lee, J.H.,Park, H.,Kim, H.W. Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate Biochem. Biophys. Res. Commun., 491:403-408, 2017 Cited by PubMed Abstract: The bacterial strain Pseudomonas sp. MC1 harbors an 81-kb metabolic plasmid, which encodes enzymes involved in the conversion of naphthalene to salicylate. Of these, the enzyme NahB (cis-dihydrodiol naphthalene dehydrogenase), which catalyzes the second reaction of this pathway, binds to various substrates such as cis-1,2-dihydro-1,2-dihydroxy-naphthalene (1,2-DDN), cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDB), and 3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl (3,4-DD-2,2',5-5-TCB). However, the mechanism underlying its broad substrate specificity is unclear owing to the lack of structural information. Here, we determined the first crystal structures of NahB in the absence and presence of NAD and 2,3-dihydroxybiphenyl (2,3-DB). Structure analysis suggests that the flexible substrate-binding loop allows NahB to accommodate diverse substrates. Furthermore, we defined the initial steps of substrate recognition and identified the early substrate-binding site in the substrate recognition process through the complex structure with ligands. PubMed: 28728845DOI: 10.1016/j.bbrc.2017.07.089 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.318 Å) |
Structure validation
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