Dehydroalanine intermediate of the FlgE D2 domain

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure and chemistry of lysinoalanine crosslinking in the spirochaete flagella hook.

Lynch, M.J.Miller, M.James, M.Zhang, S.Zhang, K.Li, C.Charon, N.W.Crane, B.R.

(2019) Nat Chem Biol 15: 959-965

  • DOI: https://doi.org/10.1038/s41589-019-0341-3
  • Primary Citation of Related Structures:  
    6NDT, 6NDV, 6NDW, 6NDX

  • PubMed Abstract: 

    The flagellar hook protein FlgE from spirochaete bacteria self-catalyzes the formation of an unusual inter-subunit lysinoalanine (Lal) crosslink that is critical for cell motility. Unlike other known examples of Lal biosynthesis, conserved cysteine and lysine residues in FlgE spontaneously react to form Lal without the involvement of additional enzymes. Oligomerization of FlgE via its D0 and Dc domains drives assembly of the crosslinking site at the D1-D2 domain interface. Structures of the FlgE D2 domain, dehydroalanine (DHA) intermediate and Lal crosslinked FlgE subunits reveal successive snapshots of the reaction. Cys178 flips from a buried configuration to release hydrogen sulfide (H 2 S/HS - ) and produce DHA. Interface residues provide hydrogen bonds to anchor the active site, facilitate β-elimination of Cys178 and polarize the peptide backbone to activate DHA for reaction with Lys165. Cysteine-reactive molecules accelerate DHA formation, whereas nucleophiles can intercept the DHA intermediate, thereby indicating a potential for Lal crosslink inhibitors to combat spirochaetal diseases.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellar hook protein FlgEA [auth B]178Treponema denticolaMutation(s): 0 
Gene Names: flgE
Find proteins for Q9RQB6 (Treponema denticola)
Explore Q9RQB6 
Go to UniProtKB:  Q9RQB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RQB6
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on DHA
Experimental Data & Validation

Experimental Data

  • Resolution: 1.42 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.488α = 90
b = 48.344β = 90
c = 98.946γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35-122535

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence