4F8B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M112.388538
  • Primary Citation of Related Structures:  

  • 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 subt ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH-dependent 7-cyano-7-deazaguanine reductase
A, B, C, D, E
165Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: queF (ykvM)
EC: 1.7.1.13
Find proteins for O31678 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31678
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PE4
Query on PE4

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Download CCD File 
D
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GD1
Query on GD1

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B, C, D, E
2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
7-cyano-7-deazaguanine, bound form
C7 H7 N5 O
BETPBINTBSWYLZ-QPIMQUGISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.507α = 90.00
b = 93.507β = 90.00
c = 193.696γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
Blu-Icedata collection
PHASESphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-01
    Type: Database references
  • Version 1.2: 2012-09-19
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description