2p88: Difference between revisions
New page: left|200px<br /><applet load="2p88" size="350" color="white" frame="true" align="right" spinBox="true" caption="2p88, resolution 2.40Å" /> '''Crystal structure of... |
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==Overview== | ==Overview== | ||
The protein databases contain many proteins with unknown function. A | The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Bacillus cereus atcc 14579]] | [[Category: Bacillus cereus atcc 14579]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Almo, S | [[Category: Almo, S C.]] | ||
[[Category: Fedorov, A | [[Category: Fedorov, A A.]] | ||
[[Category: Fedorov, E | [[Category: Fedorov, E V.]] | ||
[[Category: Gerlt, J | [[Category: Gerlt, J A.]] | ||
[[Category: Song, L.]] | [[Category: Song, L.]] | ||
[[Category: MG]] | [[Category: MG]] | ||
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[[Category: prediction of function]] | [[Category: prediction of function]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:26:55 2008'' | ||
Revision as of 19:27, 21 February 2008
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Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579
OverviewOverview
The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.
About this StructureAbout this Structure
2P88 is a Single protein structure of sequence from Bacillus cereus atcc 14579 with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
Prediction and assignment of function for a divergent N-succinyl amino acid racemase., Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA, Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1. PMID:17603539
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