| Title | Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii |
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| Author | Hackwon Do1, Chang Woo Lee1,2, Sung Gu Lee1,2, Hara Kang3, Chul Min Park4, Hak Jun Kim5, Hyun Park1,2*, HaJeung Park6*, and Jun Hyuck Lee1,2* |
| Address | 1Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea, 2Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea, 3Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea, 4Medicinal Chemistry Research Center, Bio-Organic Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea, 5Department of Chemistry, Pukyong National University, Busan 608-739, Republic of Korea, 6X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL 33458, USA |
| Bibliography | Journal of Microbiology, 54(2),114-121, 2016, |
| DOI | 10.1007/s12275-016-5549-2 |
| Key Words | DddC, dimethylsulfoniopropionate, methylmalonate- semialdehyde dehydrogenase, Oceanimonas doudoroffii, X-ray crystallography |
| Abstract | 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. |