Sandbox Reserved 1491: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Emeric Goetz (talk | contribs) No edit summary |
Emeric Goetz (talk | contribs) No edit summary |
||
| Line 1: | Line 1: | ||
{{Sandbox_Reserved_ESBS}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Sandbox_Reserved_ESBS}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
== | ==2xml - catalytic domain of KDM4C== | ||
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | ||
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
| Line 17: | Line 17: | ||
2xml is a monomeric domain composed of 348 amino acids. It is made up of two chains A and B. They are asymmetric, i.e. their sequence identities are below 95%. This domain is connected by a beta-hairpin to the rest of the protein. | 2xml is a monomeric domain composed of 348 amino acids. It is made up of two chains A and B. They are asymmetric, i.e. their sequence identities are below 95%. This domain is connected by a beta-hairpin to the rest of the protein. | ||
This domain of KDM4C can bind to 5 ligands: Zn2+, Ni2+, N-Oxalylglycine (or OGA), Cl- (interaction only with chain A) and 1,2-ethanediol (or EDO; only with chain A) : | This domain of KDM4C can bind to 5 ligands: Zn2+, Ni2+, N-Oxalylglycine (or OGA), Cl- (interaction only with chain A) and 1,2-ethanediol (or EDO; only with chain A) : | ||
OGA: two binding sites (chains A and B). | OGA: two binding sites (chains A and B). | ||
EDO: three binding sites, only in chain A. They are linked to 2xml by hydrogen bond. | EDO: three binding sites, only in chain A. They are linked to 2xml by hydrogen bond. | ||
Zn2+: two binding sites (chains A and B). It makes four coordination bonds : with three cysteines and one histidine. | Zn2+: two binding sites (chains A and B). It makes four coordination bonds : with three cysteines and one histidine. | ||
Ni2+ : two binding sites (chains A and B). It makes five coordination bonds : two with OGA, two with two histidine and a last one with a glutamic acid. | Ni2+ : two binding sites (chains A and B). It makes five coordination bonds : two with OGA, two with two histidine and a last one with a glutamic acid. | ||
Cl- : one binding site, only in chain A. | Cl- : one binding site, only in chain A. | ||
2xml presents, in each of the two chains, parallel β sheets around OGA, forming an hydrophobic (mainly made of aromatic acid) pocket. OGA interacts with 2xml amino acids through hydrogen bonds and coordination bonds with Ni2+. | 2xml presents, in each of the two chains, parallel β sheets around OGA, forming an hydrophobic (mainly made of aromatic acid) pocket. OGA interacts with 2xml amino acids through hydrogen bonds and coordination bonds with Ni2+. | ||
The sequence of the domain has been particularly preserved around OGA (when the protein is folded). Thus, the 3D structure has been very preserved as well, indicating us that the structure. | The sequence of the domain has been particularly preserved around OGA (when the protein is folded). Thus, the 3D structure has been very preserved as well, indicating us that the structure. | ||
