Structural studies of MenD : a crystallographic endeavor
Date
2009
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
ORCID
Type
Degree Level
Masters
Abstract
The thesis presented here describes the steps that were taken in an attempt to solve the protein structure of MenD via molecular replacement and multiple wavelength anomalous dispersion. The introduction provides background on menaquinone biosynthesis and the role of MenD in this metabolic pathway. Also, a detailed discussion of the DC Family of enzymes, a subgroup of ThDP dependent enzymes, which MenD is a part of, is included.
Utilizing various software packages a 1.9 Å data set was processed and analyzed in an attempt to provide a molecular replacement result. When molecular replacement was deemed incapable of solving the phase problem of the data set, the production of SeMet protein was attempted to allow for MAD phasing.
A homology model of MenD was produced using the program Modeller with benzaldehyde lyase as a template. A structure based sequence alignment was done with all DC Family enzymes with structures published. Then a second structure based sequence alignment was done to compare the same set to the Modeller model. This was done to gain a deeper understanding of MenD and how it interacts with its cofactors ThDP and Mg²⁺. Furthermore, these results were used to implicate potential active site residues.
Description
Keywords
enzyme, ThDP, SEPHCHC, MenD, X-ray crystallography
Citation
Degree
Master of Science (M.Sc.)
Department
Chemistry
Program
Chemistry