|Moran, Mary Ann||University of Georgia (UGA)||Principal Investigator|
|Kiene, Ronald||Dauphin Island Sea Lab (DISL)||Co-Principal Investigator|
|Whitman, William||University of Georgia (UGA)||Co-Principal Investigator|
|Rauch, Shannon||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||BCO-DMO Data Manager|
Links are provided to published protein structures for the apoenzyme DmdA from Pelagibacter ubique, as well as for DmdA co-crystals soaked with substrate DMSP or the cofactor tetrahydrofolate (THF) accessible via NCBI's Molecular Modeling Database (MMDB).
Experimental design, methods, and results are further described in:
D. J. Schuller, C. R. Reisch, M. A. Moran, W. B. Whitman, and W. N. Lanzilotta (2012). Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelegabacter ubique. Protein Science, vol. 21, p. 289. doi: 10.1002/pro.2015
See Schuller et al. 2012 for detailed methods, which are paraphrased below:
"Expression and isolation of the dimethylsulfoniopropionate-dependent demethylase (DmdA) from recombinant E. coli that expressed the P. ubique DmdA (SAR11_0246) gene was performed as previously described in Reisch et al. (2008). Crystal screening of DmdA was performed in an anaerobic chamber consisting of an atmosphere of 95% nitrogen and 5% hydrogen using the microbatch diffusion technique and an IMPAX I-5 (Douglas Instruments, East Garston, United Kingdom) crystallization robot.
In addition to the native crystals, data was also collected on crystals that had been treated with either the substrate (2 mM DMSP) or the cofactor, tetrahydrofolate (2 mM THF). In both cases a solution of mother liquor was prepared, under anaerobic conditions,containing either DMSP or THF.
All data sets were collected at the Advanced Photon SER-CAT on beamline 22-ID (http://www.ser.aps.anl.gov/). Several programs from the CCP4 program suite (CCP4 website) were employed during structure determination and refinement. Various molecular replacement attempts were made using the program PHASER."
Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB (2011). Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473:208–211. doi:10.1038/nature10078
|protein_name||Name/description of the protein structure.||text|
|taxon||Scientific name of the organism of study.||text|
|strain||Name of the bacterial strain.||text|
|PDB_ID||Protein structure ID number at the Protein Data Bank (http://www.rcsb.org/pdb/home/home.do)||unitless|
|MMDB_ID||Protein structure ID number at NCBI's Molecular Modeling Database (MMDB).||unitless|
This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database. 2020-02-23 12:17:47