User:Sean Callahan/Sandbox 1: Difference between revisions

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==Structure==
==Structure==
The LSD1 crystal structure was obtained in the presence of its FAD cofactor. To ensure proper formation, crystals were created in the presence of Hg ions. LSD1 contains both conserved and novel structural features. Its substrates are mono- or di-methylated lysine residues and its products are unmethylated or monomethylated lysines, respectively.  
The LSD1 crystal structure was obtained in the presence of its FAD cofactor. To ensure proper crystal formation, crystals were grown in the presence of Hg ions. LSD1 contains both conserved and novel structural features. Its substrates are mono- or di-methylated lysine residues and its products are demethylated or mono-methylated lysine residues, respectively.  
===N-Terminus===
===N-Terminus===
Going in order of primary structure, the first ~166 residues are believed to be unstructured and contain a nuclear localization signal. This area of the protein has also been shown to be susceptible to proteolytic cleavage, which may be to remove the localization signal and render protein inactive. However, a mutant of LSD1, which contains residues 166-852 (essentially eliminating the unstructured region) has been shown to be stable and viable when compared to wild-type LSD1 in a photometric activity assay. Unfortunately, this portion of the protein was unable to be crystallized.  
Going in order of primary structure, the first 166 residues are believed to be unstructured and contain a nuclear localization signal <ref name="Stavropoulos">PMID: 16799558</ref> This area of the protein has also been shown to be susceptible to proteolytic cleavage, which may be to remove the localization signal and render protein inactive<ref name="Stavropoulos">PMID: 16799558</ref>. However, a mutant of LSD1, which contains residues 166-852 (essentially eliminating the unstructured region) has been shown to be stable and viable when compared to wild-type LSD1 in a photometric activity assay<ref name="Stavropoulos">PMID: 16799558</ref>. Unfortunately, this portion of the protein was unable to be crystallized<ref name="Stavropoulos">PMID: 16799558</ref>.  
===SWIRM Domain===
===SWIRM Domain===
The next section of LSD1 spans residues 166-260 and is called the <scene name='81/811711/Swirm_domain/3'>SWIRM domain</scene>, named after the SWI3, RSC8 and MOIRA proteins from which it was first discovered. It is a highly conserved domain among histone binding proteins, however LSD1's SWIRM domain is unique in that it does not have a positively charged DNA binding domain on the exterior of the protein. Because of this, it believed that LSD1 does not directly bind DNA unlike other histone binding proteins <ref name="Da">PMID: 16461455</ref>. The highly conserved secondary structure of this domain is characterized by a long central helix, with two, shorter helix motifs surrounding it.
The next section of LSD1 spans residues 166-260 and is called the <scene name='81/811711/Swirm_domain/3'>SWIRM domain</scene>, named after the SWI3, RSC8 and MOIRA proteins from which it was first discovered. It is a highly conserved domain among histone binding proteins, however LSD1's SWIRM domain is unique in that it does not have a positively charged DNA binding domain on the exterior of the protein. Because of this, it believed that LSD1 does not directly bind DNA unlike other histone binding proteins <ref name="Da">PMID: 16461455</ref>. The highly conserved secondary structure of this domain is characterized by a long central helix, with two, shorter helix motifs surrounding it.
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