Sandbox 4: Difference between revisions

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The protein is associated with Pfam<ref>Finn R, Griffiths-Jones S, Bateman A. (2003). Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. Chapter 2: Unit 2.5.</ref> entry PF06983 of 3-demethylubiquinone-9 3-methyltransferases.
[[Image:1emaBiomics4.gif|350 px]]


<applet load='1tsj' size='400' frame='true' align='right' caption='1tsj, resolution 2.60Å' /> <scene name='1tsj/Evolutionary_consevation_1tsj/1'>highly preserved</scene> and negatively charged.
<center>{{Template:ColorKey_ConSurf}}</center>


Green fluorescent protein ('''GFP'''), originally isolated from the jellyfish Aequorea victoria (PDB entry [[1ema]]), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.


The potential substrate S-adenosyl-L-methionine has positive formal charge which fits the negative electrostatic potential in the potential catalytic area. The alternative substrate found by the structural homology methylglyoxal is not charged and thus less probable to attach to the potential catalytic area.


It seems more likely that Q8NX24 belongs to the Glyoxalase/bleomycin resistance protein/dioxygenase superfamily and functions as a demethylubiquinone-9 3-methyltransferase protein.
== Exploring the Structure ==
<applet load='1ema' size='300' frame='true' align='right' caption='Insert caption here' />
 
GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The
<scene name='Sandbox_4/Green_fp/1'>chromophore</scene>, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.<ref>PMID:8703075</ref>




==References==
==References==
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