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

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Title
Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate
Other Titles
Pseudomonas sp. MC1유래의 나프탈렌 분해효소에 대한 단백질 구조: 기질 결합의 초기과정
Authors
Park, Ae Kyung
Kim, Han-Woo
Park, Hyun
Lee, Jun Hyuck
Shin, Seung Chul
Roh, Soo Jung
Kim, Il-Sup
Kim, Hyun
Subject
Biochemistry & Molecular Biology; Biophysics
Keywords
Antarctica; Cis-dihydrodiol naphthalene dehydrogenase; Naphthalene; Pseudomonas sp
Issue Date
2017
Citation
Park, Ae Kyung, et al. 2017. "Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate". BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 491: 403-408.
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.
URI
http://repository.kopri.re.kr/handle/201206/6217
DOI
http://dx.doi.org/10.1016/j.bbrc.2017.07.089
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