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



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