2P88

Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579

Summary for 2P88

• Entry DOI: 10.2210/pdb2p88/pdb
• Related: 2P8B 2P8C
• Descriptor: Mandelate racemase/muconate lactonizing enzyme family protein, MAGNESIUM ION (3 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: 8
• Total formula weight: 328187.31

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

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: 17603539
DOI: 10.1038/nchembio.2007.11

Experimental method

X-RAY DIFFRACTION (2.4 Å)