2plm
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:2plm.jpg|left|200px]] | [[Image:2plm.jpg|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_2plm", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_2plm| PDB=2plm | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''Crystal structure of the protein TM0936 from Thermotoga maritima complexed with ZN and S-inosylhomocysteine''' | '''Crystal structure of the protein TM0936 from Thermotoga maritima complexed with ZN and S-inosylhomocysteine''' | ||
| Line 32: | Line 29: | ||
[[Category: Raushel, F M.]] | [[Category: Raushel, F M.]] | ||
[[Category: Shoichet, B K.]] | [[Category: Shoichet, B K.]] | ||
| - | [[Category: | + | [[Category: Amidohydrolase]] |
| - | [[Category: | + | [[Category: Function prediction]] |
| - | [[Category: | + | [[Category: Tm0936]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 13:22:17 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 10:22, 4 May 2008
Crystal structure of the protein TM0936 from Thermotoga maritima complexed with ZN and S-inosylhomocysteine
Overview
With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10(5) M(-1 )s(-1)). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.
About this Structure
2PLM is a Single protein structure of sequence from Thermotoga maritima. Full crystallographic information is available from OCA.
Reference
Structure-based activity prediction for an enzyme of unknown function., Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM, Nature. 2007 Aug 16;448(7155):775-9. Epub 2007 Jul 1. PMID:17603473 Page seeded by OCA on Sun May 4 13:22:17 2008
