Crystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase, Y60N mutant, ADP-inhibited

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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This is version 1.3 of the entry. See complete history


Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm.

Deka, R.K.Brautigam, C.A.Liu, W.Z.Tomchick, D.R.Norgard, M.V.

(2016) Microbiologyopen 5: 21-38

  • DOI: https://doi.org/10.1002/mbo3.306
  • Primary Citation of Related Structures:  
    4XGV, 4XGW, 4XGX, 4XHF

  • PubMed Abstract: 

    We recently reported a flavin-trafficking protein (Ftp) in the syphilis spirochete Treponema pallidum (Ftp_Tp) as the first bacterial metal-dependent FAD pyrophosphatase that hydrolyzes FAD into AMP and FMN in the periplasm. Orthologs of Ftp_Tp in other bacteria (formerly ApbE) appear to lack this hydrolytic activity; rather, they flavinylate the redox subunit, NqrC, via their metal-dependent FMN transferase activity. However, nothing has been known about the nature or mechanism of metal-dependent Ftp catalysis in either Nqr- or Rnf-redox-containing bacteria. In the current study, we identified a bimetal center in the crystal structure of Escherichia coli Ftp (Ftp_Ec) and show via mutagenesis that a single amino acid substitution converts it from an FAD-binding protein to a Mg(2+)-dependent FAD pyrophosphatase (Ftp_Tp-like). Furthermore, in the presence of protein substrates, both types of Ftps are capable of flavinylating periplasmic redox-carrying proteins (e.g., RnfG_Ec) via the metal-dependent covalent attachment of FMN. A high-resolution structure of the Ftp-mediated flavinylated protein of Shewanella oneidensis NqrC identified an essential lysine in phosphoester-threonyl-FMN bond formation in the posttranslationally modified flavoproteins. Together, these discoveries broaden our understanding of the physiological capabilities of the bacterial periplasm, and they also clarify a possible mechanism by which flavoproteins are generated.

  • Organizational Affiliation

    Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD:protein FMN transferase
A, B
340Escherichia coli K-12Mutation(s): 1 
Gene Names: apbEyojKyojLb2214JW5368
Find proteins for P0AB85 (Escherichia coli (strain K12))
Explore P0AB85 
Go to UniProtKB:  P0AB85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AB85
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
O [auth B]
C10 H15 N5 O10 P2
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
T [auth B],
U [auth B]
C2 H6 O2
Query on NO3

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
N O3
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
M [auth B],
N [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.583α = 90
b = 56.981β = 90
c = 224.766γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data 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: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description