2plm
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2plm |SIZE=350|CAPTION= <scene name='initialview01'>2plm</scene>, resolution 2.10Å | |PDB= 2plm |SIZE=350|CAPTION= <scene name='initialview01'>2plm</scene>, resolution 2.10Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=SIB:(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'>SIB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1j6p|1J6P]], [[1p1m|1P1M]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2plm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plm OCA], [http://www.ebi.ac.uk/pdbsum/2plm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2plm RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: Raushel, F M.]] | [[Category: Raushel, F M.]] | ||
[[Category: Shoichet, B K.]] | [[Category: Shoichet, B K.]] | ||
| - | [[Category: SIB]] | ||
| - | [[Category: ZN]] | ||
[[Category: amidohydrolase]] | [[Category: amidohydrolase]] | ||
[[Category: function prediction]] | [[Category: function prediction]] | ||
[[Category: tm0936]] | [[Category: tm0936]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:37:39 2008'' |
Revision as of 01:37, 31 March 2008
| |||||||
| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Related: | 1J6P, 1P1M
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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 Mon Mar 31 04:37:39 2008
