2P8B
Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 complexed with N-succinyl Lys.
Summary for 2P8B
| Entry DOI | 10.2210/pdb2p8b/pdb |
| Related | 2P88 2P8C |
| Descriptor | Mandelate racemase/muconate lactonizing enzyme family protein, MAGNESIUM ION, N-SUCCINYL LYSINE, ... (4 entities in total) |
| Functional Keywords | enolase superfamily, prediction of function, n-succinyl amino acid racemase, lyase |
| Biological source | Bacillus cereus ATCC 14579 |
| Total number of polymer chains | 1 |
| Total formula weight | 41269.67 |
| Authors | Fedorov, A.A.,Song, L.,Fedorov, E.V.,Gerlt, J.A.,Almo, S.C. (deposition date: 2007-03-22, release date: 2007-07-03, Last modification date: 2023-08-30) |
| Primary citation | Song, L.,Kalyanaraman, C.,Fedorov, A.A.,Fedorov, E.V.,Glasner, M.E.,Brown, S.,Imker, H.J.,Babbitt, P.C.,Almo, S.C.,Jacobson, M.P.,Gerlt, J.A. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat.Chem.Biol., 3:486-491, 2007 Cited by PubMed Abstract: 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. PubMed: 17603539DOI: 10.1038/nchembio.2007.11 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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