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: 1.901 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


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:  

  • 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 dihydromethanopt ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative dihydromethanopterin reductase (AfpA)
A
199Paraburkholderia xenovorans (strain LB400)Mutation(s): 0 
Find proteins for Q13QT8 (Paraburkholderia xenovorans (strain LB400))
Go to UniProtKB:  Q13QT8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd: 40 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 183.840α = 90.00
b = 183.840β = 90.00
c = 183.840γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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