A. aeolicus BioW with pimelate

Experimental Data Snapshot

  • Resolution: 2.46 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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This is version 1.3 of the entry. See complete history


The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes.

Estrada, P.Manandhar, M.Dong, S.H.Deveryshetty, J.Agarwal, V.Cronan, J.E.Nair, S.K.

(2017) Nat Chem Biol 13: 668-674

  • DOI: https://doi.org/10.1038/nchembio.2359
  • Primary Citation of Related Structures:  
    5TV5, 5TV6, 5TV8, 5TVA

  • PubMed Abstract: 

    Reactions that activate carboxylates through acyl-adenylate intermediates are found throughout biology and include acyl- and aryl-CoA synthetases and tRNA synthetases. Here we describe the characterization of Aquifex aeolicus BioW, which represents a new protein fold within the superfamily of adenylating enzymes. Substrate-bound structures identified the enzyme active site and elucidated the mechanistic strategy for conjugating CoA to the seven-carbon α,ω-dicarboxylate pimelate, a biotin precursor. Proper position of reactive groups for the two half-reactions is achieved solely through movements of active site residues, as confirmed by site-directed mutational analysis. The ability of BioW to hydrolyze adenylates of noncognate substrates is reminiscent of pre-transfer proofreading observed in some tRNA synthetases, and we show that this activity can be abolished by mutation of a single residue. These studies illustrate how BioW can carry out three different biologically prevalent chemical reactions (adenylation, thioesterification, and proofreading) in the context of a new protein fold.

  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-carboxyhexanoate--CoA ligase
A, B
240Aquifex aeolicusMutation(s): 0 
Gene Names: bioWaq_1659
Find proteins for O67575 (Aquifex aeolicus (strain VF5))
Explore O67575 
Go to UniProtKB:  O67575
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67575
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.46 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.486α = 90
b = 103.194β = 90
c = 113.805γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-05-03
    Changes: Database references
  • Version 1.3: 2017-05-31
    Changes: Database references