2P88: Crystal Structure Of N-succinyl Arg/lys Racemase From Bacillus Cereus Atcc 14579

Citation:
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.
PDB ID: 2P88Download
MMDB ID: 47213
PDB Deposition Date: 2007/3/22
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Similar Structures:
Biological Unit for 2P88: octameric; determined by author
Molecular Components in 2P88
Label Count Molecule
Proteins (8 molecules)
8
Mandelate Racemase/muconate Lactonizing Enzyme Family Protein(Gene symbol: BC0371)
Molecule annotation
Chemicals (8 molecules)
1
8
* Click molecule labels to explore molecular sequence information.

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