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Biochem Biophys Res Commun. 2017 Sep 16;491(2):403-408. doi: 10.1016/j.bbrc.2017.07.089. Epub 2017 Jul 17.

Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate.

Author information

1
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, South Korea.
2
School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, South Korea.
3
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, South Korea; Evolutionary Genomics Laboratory, Department of Biological Sciences, Inha University, 100 Inha-ro, Nam-gu, Incheon, 22212, South Korea.
4
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, South Korea.
5
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, South Korea. Electronic address: hwkim@kopri.re.kr.

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.

KEYWORDS:

2,3-Dihydroxybiphenyl; Antarctica; Cis-dihydrodiol naphthalene dehydrogenase; Degradation; Naphthalene; Pseudomonas sp.

PMID:
28728845
DOI:
10.1016/j.bbrc.2017.07.089
[Indexed for MEDLINE]

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