2P8B

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Prediction and assignment of function for a divergent N-succinyl amino acid racemase.

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.

(2007) Nat.Chem.Biol. 3: 486-491

  • DOI: 10.1038/nchembio.2007.11
  • Primary Citation of Related Structures:  

  • 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 functi ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mandelate racemase/muconate lactonizing enzyme family protein
A
369Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)Mutation(s): 0 
EC: 5.1.1.-
Find proteins for Q81IL5 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Go to UniProtKB:  Q81IL5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NSK
Query on NSK
Download SDF File 
Download CCD File 
A
N-SUCCINYL LYSINE
N~2~-(3-CARBOXYPROPANOYL)-L-LYSINE
C10 H18 N2 O5
XEOGRHZGJFTETQ-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.206 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 134.924α = 90.00
b = 134.924β = 90.00
c = 96.791γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-01-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance