2PLM

Crystal structure of the protein TM0936 from Thermotoga maritima complexed with ZN and S-inosylhomocysteine

Summary for 2PLM

• Entry DOI: 10.2210/pdb2plm/pdb
• Related: 1J6P 1P1M
• Descriptor: Uncharacterized protein, ZINC ION, (2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID, ... (4 entities in total)
• Functional Keywords: tm0936, function prediction, amidohydrolase, unknown function
• Biological source: Thermotoga maritima
• Total number of polymer chains: 1
• Total formula weight: 46275.16

Authors

Fedorov, A.A.,Fedorov, E.V.,Hermann, J.C.,Marti-Arbona, R.,Shoichet, B.K.,Raushel, F.M.,Almo, S.C. (deposition date: 2007-04-20, release date: 2007-07-17, Last modification date: 2023-08-30)

Primary citation

Hermann, J.C.,Marti-Arbona, R.,Fedorov, A.A.,Fedorov, E.,Almo, S.C.,Shoichet, B.K.,Raushel, F.M.
Structure-based activity prediction for an enzyme of unknown function
Nature, 448:775-779, 2007

PubMed Abstract: 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.

PubMed: 17603473
DOI: 10.1038/nature05981

Experimental method

X-RAY DIFFRACTION (2.1 Å)