title: Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii.
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 NAD-dependent 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.
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.
authors.forename: Hackwon
authors.initials: H
authors.lastname: Do
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.|Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.
authors.forename: Chang Woo
authors.initials: CW
authors.lastname: Lee
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.|Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.
authors.forename: Sung Gu
authors.initials: SG
authors.lastname: Lee
authors.affiliation: Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea.
authors.forename: Hara
authors.initials: H
authors.lastname: Kang
authors.affiliation: Medicinal Chemistry Research Center, Bio-Organic Division, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Republic of Korea.
authors.forename: Chul Min
authors.initials: CM
authors.lastname: Park
authors.affiliation: Department of Chemistry, Pukyong National University, Busan, 608-739, Republic of Korea.
authors.forename: Hak Jun
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. hpark@kopri.re.kr.|Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea. hpark@kopri.re.kr.
authors.forename: Hyun
authors.initials: H
authors.lastname: Park
authors.affiliation: X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL, 33458, USA. hajpark@scripps.edu.
authors.forename: HaJeung
authors.initials: H
authors.lastname: Park
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. junhyucklee@kopri.re.kr.|Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea. junhyucklee@kopri.re.kr.
authors.forename: Jun Hyuck
authors.initials: JH
authors.lastname: Lee
mesh_terms: D044044:Aeromonadaceae / Q000201:enzymology*; D018360:Crystallography, X-Ray; D050646:Methylmalonate-Semialdehyde Dehydrogenase (Acylating) / Q000737:chemistry*; D008958:Models, Molecular; D009243:NAD / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary
chemical_list: D009243:NAD; D050646:Methylmalonate-Semialdehyde Dehydrogenase (Acylating)
keywords: DddC; Oceanimonas doudoroffii; X-ray crystallography; dimethylsulfoniopropionate; methylmalonate-semialdehyde dehydrogenase
references.citation: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):271-81
references.pmid: 21460445
references.citation: Protein Sci. 1993 Nov;2(11):1890-900
references.pmid: 8268800
references.citation: Structure. 1997 May 15;5(5):701-11
references.pmid: 9195888
references.citation: Environ Microbiol. 2010 Feb;12 (2):327-43
references.pmid: 19807777
references.citation: J Biol Chem. 1992 Jul 5;267(19):13585-92
references.pmid: 1339433
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21
references.pmid: 20057044
references.citation: Environ Microbiol. 2011 Feb;13(2):427-38
references.pmid: 20880330
references.citation: J Biol Chem. 2012 Sep 7;287(37):31095-103
references.pmid: 22782904
references.citation: J Biol Chem. 1970 Apr 10;245(7):1828-35
references.pmid: 4314598
references.citation: Front Microbiol. 2011 Aug 12;2:172
references.pmid: 21886640
references.citation: Nat Struct Biol. 1997 Apr;4(4):317-26
references.pmid: 9095201
references.citation: J Bacteriol. 1996 Jan;178(2):490-5
references.pmid: 8550471
references.citation: Protein Sci. 1999 Dec;8(12):2784-90
references.pmid: 10631996
references.citation: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42
references.pmid: 21460441
references.citation: ISME J. 2012 Jan;6(1):223-6
references.pmid: 21677693
references.citation: Biochem J. 2006 Apr 1;395(1):107-15
references.pmid: 16332250
references.citation: ISME J. 2011 Jul;5(7):1191-200
references.pmid: 21248856
references.citation: Structure. 2013 Nov 5;21(11):1923-30
references.pmid: 24076406
references.citation: Hum Genomics. 2005 Jun;2(2):138-43
references.pmid: 16004729
references.citation: Protein Sci. 1998 Oct;7(10):2106-17
references.pmid: 9792097
references.citation: Nat Rev Microbiol. 2011 Oct 11;9(12 ):849-59
references.pmid: 21986900
references.citation: Nature. 2002 Jul 18;418(6895):317-20
references.pmid: 12124622
references.citation: Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54
references.pmid: 12393927
references.citation: J Biol Chem. 2011 Jun 24;286(25):21971-81
references.pmid: 21515690
references.citation: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
references.pmid: 21460454
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765