Sandbox reserved 330: Difference between revisions
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Crystallization of the YdcE gene product revealed a crystal with space group of P6522, where a= 56.63, b=56.63, and c=138.257. The final structure model of the YdcE protein was determined to be 2.1 A with an R-factor of 15.9%. The YdcE protein consists of 117 amino acids and is approximately 14 kDa. It is a compact single domain alpha/beta protein, with 3 α helices and 7 β strands. Five out of seven beta strands, β1, β2, β3, β6, and β7 forms an antiparallel sheet. While two of the remaining strands, β4, β5, and C terminus (containing Asp115) of the β3 strand forms a smaller sheet. | Crystallization of the YdcE gene product revealed a crystal with space group of P6522, where a= 56.63, b=56.63, and c=138.257. The final structure model of the YdcE protein was determined to be 2.1 A with an R-factor of 15.9%. The YdcE protein consists of 117 amino acids and is approximately 14 kDa. It is a compact single domain alpha/beta protein, with 3 α helices and 7 β strands. Five out of seven beta strands, β1, β2, β3, β6, and β7 forms an antiparallel sheet. While two of the remaining strands, β4, β5, and C terminus (containing Asp115) of the β3 strand forms a smaller sheet. | ||
[[Image:Hydrophobic_residues.jpg | thumb | right | 380px |Amino acids on extensive hydrophobic surface]] | |||
The structure itself is a dimer interface between monomers that is related by a two fold axis, and it exists as a dimer in solution as well. The dimer is a convex surface with a flat surface that includes 3 α helix that has C-terminal tails protruding. The convex surface is an extensive hydrophobic surface between the two monomers, and include Ile 30, Ile 43, Ile 111, Leu 107, Ile 80 and Ile 114. Each monomer has a β6 strand that is paired with each other through hydrogen bonds between the amide of the Thr82 and the carbonyl oxygen of Ile 80. On the convex side of the dimer, hydrogen bonds exist between amides of Ser 19, to the side chain of Asp 84, along with salt bridges between Glu 20 and Arg 87. Between these salt bridges, the Arg 81 of each monomer are buried in the dimer interface and is stabilized by water-mediated hydrogen bonds. Other dimer interactions of the YdcE protein include a hydrogen bond between carbonyl oxygen of Ser 110 and the amide of Asn 32, and between the carbonyl oxygen of Ala 112 and NE of Arg5. | The structure itself is a dimer interface between monomers that is related by a two fold axis, and it exists as a dimer in solution as well. The dimer is a convex surface with a flat surface that includes 3 α helix that has C-terminal tails protruding. The convex surface is an extensive hydrophobic surface between the two monomers, and include Ile 30, Ile 43, Ile 111, Leu 107, Ile 80 and Ile 114. Each monomer has a β6 strand that is paired with each other through hydrogen bonds between the amide of the Thr82 and the carbonyl oxygen of Ile 80. On the convex side of the dimer, hydrogen bonds exist between amides of Ser 19, to the side chain of Asp 84, along with salt bridges between Glu 20 and Arg 87. Between these salt bridges, the Arg 81 of each monomer are buried in the dimer interface and is stabilized by water-mediated hydrogen bonds. Other dimer interactions of the YdcE protein include a hydrogen bond between carbonyl oxygen of Ser 110 and the amide of Asn 32, and between the carbonyl oxygen of Ala 112 and NE of Arg5. | ||
The YcdE protein has similar structures to other proteins, such as Pem/Kid from E.coli in plasmid R1, and CcdB from E.coli in plasmid F. These similarities include a five stranded antiparallel sheet and a smaller three stranded β-sheet with a C-terminal α helix. YdcE shares 27% sequence similarity with Pem/Kid and 7% with CcdB. However, the electronegative surface potential of YdcE is more negative than Kid and CcdB, with a pI of 4.7. This is largely due to having six charged amino acids; Asp 96, Asp 97, Glu 98, Glu 105, Asp 101, and Asp 104. | The YcdE protein has similar structures to other proteins, such as Pem/Kid from E.coli in plasmid R1, and CcdB from E.coli in plasmid F. These similarities include a five stranded antiparallel sheet and a smaller three stranded β-sheet with a C-terminal α helix. YdcE shares 27% sequence similarity with Pem/Kid and 7% with CcdB. However, the electronegative surface potential of YdcE is more negative than Kid and CcdB, with a pI of 4.7. This is largely due to having six charged amino acids; Asp 96, Asp 97, Glu 98, Glu 105, Asp 101, and Asp 104. | ||
[[Image:6_charged_AA.jpg | thumb | right | 380px |6 charged amino acids contributing to electronegative surface potential]] | [[Image:6_charged_AA.jpg | thumb | right | 380px |6 charged amino acids contributing to electronegative surface potential]] | ||
