1SJB

X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis

Thoden, J.B.Taylor-Ringia, E.A.Garrett, J.B.Gerlt, J.A.Holden, H.M.Rayment, I.

(2004) Biochemistry 43: 5716-5727

  • DOI: 10.1021/bi0497897
  • Primary Citation of Related Structures:  1SJA, 1SJC, 1SJD

  • PubMed Abstract: 
  • Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated ...

    Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality.


    Organizational Affiliation

    Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acylamino acid racemase
A, B, C, D
368Amycolatopsis sp.Gene Names: Aaar (menC)
EC: 4.2.1.113
Find proteins for Q44244 (Amycolatopsis sp.)
Go to UniProtKB:  Q44244
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OSB
Query on OSB

Download SDF File 
Download CCD File 
A, B, C, D
2-SUCCINYLBENZOATE
O-SUCCINYLBENZOATE
C11 H10 O5
YIVWQNVQRXFZJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 216.000α = 90.00
b = 216.000β = 90.00
c = 261.000γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata reduction
HKL-2000data scaling
TNTrefinement
HKL-2000data reduction
d*TREKdata scaling
TNTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance