1WUE

Crystal structure of protein GI:29375081, unknown member of enolase superfamily from enterococcus faecalis V583

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.7 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: 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 ...

    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; margy.glasner@tamu.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mandelate racemase/muconate lactonizing enzyme family proteinA, B386Enterococcus faecalis V583Mutation(s): 0 
Gene Names: menC, EF_0450
EC: 4.2.1.113
UniProt
Find proteins for Q838J7 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q838J7 
Go to UniProtKB:  Q838J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ838J7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.807α = 90
b = 136.807β = 90
c = 112.771γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2014-06-11
    Changes: Database references
  • Version 1.4: 2014-06-18
    Changes: Other
  • Version 1.5: 2014-12-24
    Changes: Database references
  • Version 1.6: 2017-12-20
    Changes: Database references
  • Version 1.7: 2021-02-03
    Changes: Database references, Structure summary