4ZZ7

Crystal structure of methylmalonate-semialdehyde dehydrogenase (DddC) from Oceanimonas doudoroffii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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

Do, H.Lee, C.W.Lee, S.G.Kang, H.Park, C.M.Kim, H.J.Park, H.Park, H.Lee, J.H.

(2016) J. Microbiol. 54: 114-121

  • DOI: 10.1007/s12275-016-5549-2

  • PubMed 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 cat ...

    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.


    Organizational Affiliation

    Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea. hpark@kopri.re.kr.,Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea. junhyucklee@kopri.re.kr.,Department of Chemistry, Pukyong National University, Busan, 608-739, Republic of Korea.,Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Republic of Korea.,X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL, 33458, USA. hajpark@scripps.edu.,Department of Polar Sciences, University of Science and Technology, Incheon, 406-840, Republic of Korea.,Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea.,Medicinal Chemistry Research Center, Bio-Organic Division, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Republic of Korea.,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. junhyucklee@kopri.re.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylmalonate-semialdehyde dehydrogenase
A, B, C, D, E, F, G, H, I, J, K, L
501Oceanimonas doudoroffiiMutation(s): 0 
Gene Names: dddC (mmsA)
Find proteins for G5CZI2 (Oceanimonas doudoroffii)
Go to UniProtKB:  G5CZI2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, C, D, E, I, L
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 156.700α = 90.00
b = 160.300β = 90.00
c = 238.920γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Korea Polar Research InstituteKorea, Republic OfPE15070

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release