4IFX

Crystal structure of Treponema pallidum TP0796 Flavin trafficking protein, FAD substrate bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis.

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

(2013) J Biol Chem 288: 11106-11121

  • DOI: https://doi.org/10.1074/jbc.M113.449975
  • Primary Citation of Related Structures:  
    4IFU, 4IFW, 4IFX, 4IFZ, 4IG1

  • PubMed Abstract: 

    Treponema pallidum, an obligate parasite of humans and the causative agent of syphilis, has evolved the capacity to exploit host-derived metabolites for its survival. Flavin-containing compounds are essential cofactors that are required for metabolic processes in all living organisms, and riboflavin is a direct precursor of the cofactors FMN and FAD. Unlike many pathogenic bacteria, Treponema pallidum cannot synthesize riboflavin; we recently described a flavin-uptake mechanism composed of an ABC-type transporter. However, there is a paucity of information about flavin utilization in bacterial periplasms. Using a discovery-driven approach, we have identified the TP0796 lipoprotein as a previously uncharacterized Mg(2+)-dependent FAD pyrophosphatase within the ApbE superfamily. TP0796 probably plays a central role in flavin turnover by hydrolyzing exogenously acquired FAD, yielding AMP and FMN. Biochemical and structural investigations revealed that the enzyme has a unique bimetal Mg(2+) catalytic center. Furthermore, the pyrophosphatase activity is product-inhibited by AMP, indicating a possible role for this molecule in modulating FMN and FAD levels in the treponemal periplasm. The ApbE superfamily was previously thought to be involved in thiamine biosynthesis, but our characterization of TP0796 prompts a renaming of this superfamily as a periplasmic flavin-trafficking protein (Ftp). TP0796 is the first structurally and biochemically characterized FAD pyrophosphate enzyme in bacteria. This new paradigm for a bacterial flavin utilization pathway may prove to be useful for future inhibitor design.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine biosynthesis lipoprotein ApbE340Treponema pallidum subsp. pallidum str. NicholsMutation(s): 0 
Gene Names: apbEtp0796TP_0796
UniProt
Find proteins for O83774 (Treponema pallidum (strain Nichols))
Explore O83774 
Go to UniProtKB:  O83774
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO83774
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.825α = 90
b = 47.079β = 102
c = 57.583γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
DENZOdata reduction
HKL-3000data scaling
PHENIXphasing
SCALEPACKdata 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: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Structure summary
  • Version 1.2: 2013-03-13
    Changes: Database references
  • Version 1.3: 2013-05-08
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.6: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description