Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii

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• 作者：Hackwon Do ; Chang Woo Lee ; Sung Gu Lee ; Hara Kang ; Chul Min Park…
• 关键词：DddC ; dimethylsulfoniopropionate ; methylmalonate ; semialdehyde dehydrogenase ; Oceanimonas doudoroffii ; X ; ray crystallography
• 刊名：Journal of Microbiology
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：54
• 期：2
• 页码：114-121
• 全文大小：960 KB
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• 作者单位：Hackwon Do (1)
  Chang Woo Lee (1) (2)
  Sung Gu Lee (1) (2)
  Hara Kang (3)
  Chul Min Park (4)
  Hak Jun Kim (5)
  Hyun Park (1) (2)
  HaJeung Park (6)
  Jun Hyuck Lee (1) (2)
  
  1. Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea
  2. Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea
  3. Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea
  4. Medicinal Chemistry Research Center, Bio-Organic Division, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Republic of Korea
  5. Department of Chemistry, Pukyong National University, Busan, 608-739, Republic of Korea
  6. X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL, 33458, USA
  
• 刊物主题：Microbiology;
• 出版者：Springer Netherlands
• ISSN：1976-3794

文摘

The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NADdependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH. Keywords DddC dimethylsulfoniopropionate methylmalonate-semialdehyde dehydrogenase Oceanimonas doudoroffii X-ray crystallography