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Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8535-40. doi: 10.1073/pnas.1318703111. Epub 2014 May 28.

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

Author information

  • 1Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128;
  • 2Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
  • 3Departments of Biochemistry and.
  • 4Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973;
  • 5Department of Biochemistry, National University of Singapore, Singapore 117597;
  • 6Lilly Biotechnology Center, San Diego, CA 92121;
  • 7BioMaPS Institute for Quantitative Biology,Research Collaboratory for Structural Bioinformatics Protein Data Bank,Center for Integrative Proteomics Research,Rutgers Cancer Institute of New Jersey, andDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8076.
  • 8Departments of Biochemistry andPhysiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461;
  • 9Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128; margy.glasner@tamu.edu.

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.

KEYWORDS:

enolase superfamily; protein structure; protein structure-function relationships

PMID:
24872444
[PubMed - indexed for MEDLINE]
PMCID:
PMC4060685
Free PMC Article
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