4F8B

Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

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This is version 1.4 of the entry. See complete history


Literature

Structural basis of biological nitrile reduction.

Chikwana, V.M.Stec, B.Lee, B.W.de Crecy-Lagard, V.Iwata-Reuyl, D.Swairjo, M.A.

(2012) J Biol Chem 287: 30560-30570

  • DOI: https://doi.org/10.1074/jbc.M112.388538
  • Primary Citation of Related Structures:  
    4F8B, 4FGC

  • PubMed Abstract: 

    The enzyme QueF catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ(0)) to 7-aminomethyl-7-deazaguanine (preQ(1)), the only nitrile reduction reaction known in biology. We describe here two crystal structures of Bacillus subtilis QueF, one of the wild-type enzyme in complex with the substrate preQ(0), trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the C55A mutant in complex with the substrate preQ(0) bound noncovalently. The QueF enzyme forms an asymmetric tunnel-fold homodecamer of two head-to-head facing pentameric subunits, harboring 10 active sites at the intersubunit interfaces. In both structures, a preQ(0) molecule is bound at eight sites, and in the wild-type enzyme, it forms a thioimide covalent linkage to the catalytic residue Cys-55. Both structural and transient kinetic data show that preQ(0) binding, not thioimide formation, induces a large conformational change in and closure of the active site. Based on these data, we propose a mechanism for the activation of the Cys-55 nucleophile and subsequent hydride transfer.


  • Organizational Affiliation

    Department of Chemistry, Portland State University, Portland, OR 97207, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADPH-dependent 7-cyano-7-deazaguanine reductase
A, B, C, D, E
165Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU13750queFykvM
EC: 1.7.1.13
UniProt
Find proteins for O31678 (Bacillus subtilis (strain 168))
Explore O31678 
Go to UniProtKB:  O31678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31678
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
M [auth D]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
GD1
Query on GD1

Download Ideal Coordinates CCD File 
F [auth B],
I [auth C],
K [auth D],
N [auth E]
2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
C7 H7 N5 O
BETPBINTBSWYLZ-QPIMQUGISA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B],
J [auth C],
L [auth D],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.507α = 90
b = 93.507β = 90
c = 193.696γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references
  • Version 1.2: 2012-09-19
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description