3WIS

Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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This is version 1.3 of the entry. See complete history


Literature

Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer

Mcnamara, D.E.Cascio, D.Jorda, J.Bustos, C.Wang, T.C.Rasche, M.E.Yeates, T.O.Bobik, T.A.

(2014) J Biol Chem 289: 8852-8864

  • DOI: 10.1074/jbc.M113.522342
  • Primary Citation of Related Structures:  
    3WIS, 4MWG

  • PubMed Abstract: 
  • Dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism by archaea and some bacteria. DmrB is a bacterial enzyme understood to reduce dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents, but the mechanistic details have not been elucidated previously ...

    Dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism by archaea and some bacteria. DmrB is a bacterial enzyme understood to reduce dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents, but the mechanistic details have not been elucidated previously. Here we report the crystal structure of DmrB from Burkholderia xenovorans at a resolution of 1.9 Å. Unexpectedly, the biological unit is a 24-mer composed of eight homotrimers located at the corners of a cubic cage-like structure. Within a homotrimer, each monomer-monomer interface exhibits an active site with two adjacently bound flavin mononucleotide (FMN) ligands, one deeply buried and tightly bound and one more peripheral, for a total of 48 ligands in the biological unit. Computational docking suggested that the peripheral site could bind either the observed FMN (the electron donor for the overall reaction) or the pterin, H2MPT (the electron acceptor for the overall reaction), in configurations ideal for electron transfer to and from the tightly bound FMN. On this basis, we propose that DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate. Sequence comparisons suggested that the catalytic mechanism is conserved among the bacterial homologs of DmrB and partially conserved in archaeal homologs, where an alternate electron donor is likely used. In addition to the mechanistic revelations, the structure of DmrB could help guide the development of anti-obesity drugs based on modification of the ecology of the human gut.


    Organizational Affiliation

    From the Department of Chemistry and Biochemistry.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative dihydromethanopterin reductase (AfpA)A199Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: Bxeno_B0583Bxe_B2440DmrB
UniProt
Find proteins for Q13QT8 (Paraburkholderia xenovorans (strain LB400))
Explore Q13QT8 
Go to UniProtKB:  Q13QT8
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FMN Binding MOAD:  3WIS Kd: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.84α = 90
b = 183.84β = 90
c = 183.84γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXCDphasing
SHELXEmodel building

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2014-04-23
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description