3PKV

Crystal Structure of Toxoflavin Lyase (TflA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Toxoflavin lyase requires a novel 1-his-2-carboxylate facial triad .

Fenwick, M.K.Philmus, B.Begley, T.P.Ealick, S.E.

(2011) Biochemistry 50: 1091-1100

  • DOI: 10.1021/bi101741v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High-resolution crystal structures are reported for apo, holo, and substrate-bound forms of a toxoflavin-degrading metalloenzyme (TflA). In addition, the degradation reaction is shown to be dependent on oxygen, Mn(II), and dithiothreitol in vitro. De ...

    High-resolution crystal structures are reported for apo, holo, and substrate-bound forms of a toxoflavin-degrading metalloenzyme (TflA). In addition, the degradation reaction is shown to be dependent on oxygen, Mn(II), and dithiothreitol in vitro. Despite its low sequence identity with proteins of known structure, TflA is structurally homologous to proteins of the vicinal oxygen chelate superfamily. Like other metalloenzymes in this superfamily, the TflA fold contains four modules that associate to form a metal binding site; however, the fold displays a rare rearrangement of the structural modules indicative of domain permutation. Moreover, unlike the 2-His-1-carboxylate facial triad commonly utilized by vicinal oxygen chelate dioxygenases and other dioxygen-activating non-heme Fe(II) enzymes, the metal center in TflA consists of a 1-His-2-carboxylate facial triad. The substrate-bound complex shows square-pyramidal geometry in which one position is occupied by O5 of toxoflavin. The open coordination site is predicted to be the dioxygen binding site. TflA appears to stabilize the reduced form of toxoflavin through second-sphere interactions. This anionic species is predicted to be the electron source responsible for reductive activation of oxygen to produce a peroxytoxoflavin intermediate.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxoflavin lyase (TflA)
A
252Paenibacillus polymyxaMutation(s): 0 
Gene Names: tflA
Find proteins for E3SET7 (Paenibacillus polymyxa)
Go to UniProtKB:  E3SET7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 110.581α = 90.00
b = 110.581β = 90.00
c = 58.069γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
HKL-2000data reduction
DENZOdata reduction
SHELXphasing
HKL-2000data scaling
SHELXDphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description