4NJG

Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet and 6-carboxypterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.

Dowling, D.P.Bruender, N.A.Young, A.P.McCarty, R.M.Bandarian, V.Drennan, C.L.

(2014) Nat.Chem.Biol. 10: 106-112

  • DOI: 10.1038/nchembio.1426
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg(2+)-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a me ...

    7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg(2+)-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a member of the AdoMet radical superfamily, which employs the 5'-deoxyadenosyl radical from reductive cleavage of AdoMet to initiate chemistry. To provide a mechanistic rationale for this elaborate transformation, we present the crystal structure of a QueE along with structures of pre- and post-turnover states. We find that substrate binds perpendicular to the [4Fe-4S]-bound AdoMet, exposing its C6 hydrogen atom for abstraction and generating the binding site for Mg(2+), which coordinates directly to the substrate. The Burkholderia multivorans structure reported here varies from all other previously characterized members of the AdoMet radical superfamily in that it contains a hypermodified (β6/α3) protein core and an expanded cluster-binding motif, CX14CX2C.


    Organizational Affiliation

    1] Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7-carboxy-7-deazaguanine synthase
A, B
230Burkholderia multivorans (strain ATCC 17616 / 249)Mutation(s): 0 
Gene Names: queE
EC: 4.3.99.3
Find proteins for A0A0H3KB22 (Burkholderia multivorans (strain ATCC 17616 / 249))
Go to UniProtKB:  A0A0H3KB22
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HHS
Query on HHS

Download SDF File 
Download CCD File 
A, B
6-CARBOXYPTERIN
2-amino-4-oxo-3,4-dihydropteridine-6-carboxylic acid
C7 H5 N5 O3
QABAUCFGPWONOG-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 118.956α = 90.00
b = 118.956β = 90.00
c = 101.952γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CBASSdata collection
SHARPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Database references