5TGS

Crystal Structure of QueE from Bacillus subtilis with methionine bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.548 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies.

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

(2017) J. Am. Chem. Soc. 139: 1912-1920

  • DOI: 10.1021/jacs.6b11381
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Radical S-adenosyl-l-methionine (SAM) enzymes are widely distributed and catalyze diverse reactions. SAM binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster and is reductively cleaved to generate a 5'-deoxyadenosyl radical, which ...

    Radical S-adenosyl-l-methionine (SAM) enzymes are widely distributed and catalyze diverse reactions. SAM binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster and is reductively cleaved to generate a 5'-deoxyadenosyl radical, which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes a key step in the biosynthesis of 7-deazapurine containing natural products. 6-Carboxypterin (6-CP), an oxidized analogue of the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase. Under reducing conditions that would promote the reductive cleavage of SAM, 6-CP is turned over to 6-deoxyadenosylpterin (6-dAP), presumably by radical addition of the 5'-deoxyadenosine followed by oxidative decarboxylation to the product. By contrast, in the absence of the strong reductant, dithionite, the carboxylate of 6-CP is esterified to generate 6-carboxypterin-5'-deoxyadenosyl ester (6-CP-dAdo ester). Structural studies with 6-CP and SAM also reveal electron density consistent with the ester product being formed in crystallo. The differential reactivity of 6-CP under reducing and nonreducing conditions highlights the ability of radical SAM enzymes to carry out both polar and radical transformations in the same active site.


    Organizational Affiliation

    Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7-carboxy-7-deazaguanine synthase
A, B
263Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: queE (ykvL)
EC: 4.3.99.3
Find proteins for O31677 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31677
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
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.548 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.182α = 90.00
b = 79.297β = 90.00
c = 122.224γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
SHARPphasing
Cootmodel building
autoSHARPphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM72623
National Science Foundation (United States)United States1122374

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Database references
  • Version 1.2: 2017-02-15
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence