3CAW

Crystal structure of o-succinylbenzoate synthase from Bdellovibrio bacteriovorus liganded with Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.

Odokonyero, D.Sakai, A.Patskovsky, Y.Malashkevich, V.N.Fedorov, A.A.Bonanno, J.B.Fedorov, E.V.Toro, R.Agarwal, R.Wang, C.Ozerova, N.D.Yew, W.S.Sauder, J.M.Swaminathan, S.Burley, S.K.Almo, S.C.Glasner, M.E.

(2014) Proc Natl Acad Sci U S A 111: 8535-8540

  • DOI: https://doi.org/10.1073/pnas.1318703111
  • Primary Citation of Related Structures:  
    1WUE, 1WUF, 2OKT, 2OLA, 2OZT, 2PGE, 3CAW, 3H70, 3H7V

  • PubMed Abstract: 

    The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
o-succinylbenzoate synthase
A, B
330Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd0547
UniProt
Find proteins for Q6MQC7 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MQC7 
Go to UniProtKB:  Q6MQC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MQC7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.381α = 90
b = 78.61β = 91.78
c = 78.462γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-06-11
    Changes: Database references
  • Version 1.3: 2014-08-13
    Changes: Database references
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references