3BP1

Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism.

Kim, Y.Zhou, M.Moy, S.Morales, J.Cunningham, M.A.Joachimiak, A.

(2010) J Mol Biol 404: 127-137

  • DOI: https://doi.org/10.1016/j.jmb.2010.09.042
  • Primary Citation of Related Structures:  
    3BP1

  • PubMed Abstract: 

    Here, we report the 1.53-Å crystal structure of the enzyme 7-cyano-7-deazaguanine reductase (QueF) from Vibrio cholerae, which is responsible for the complete reduction of a nitrile (CN) bond to a primary amine (H(2)C-NH(2)). At present, this is the only example of a biological pathway that includes reduction of a nitrile bond, establishing QueF as particularly noteworthy. The structure of the QueF monomer resembles two connected ferrodoxin-like domains that assemble into dimers. Ligands identified in the crystal structure suggest the likely binding conformation of the native substrates NADPH and 7-cyano-7-deazaguanine. We also report on a series of numerical simulations that have shed light on the mechanism by which this enzyme affects the transfer of four protons (and electrons) to the 7-cyano-7-deazaguanine substrate. In particular, the simulations suggest that the initial step of the catalytic process is the formation of a covalent adduct with the residue Cys194, in agreement with previous studies. The crystal structure also suggests that two conserved residues (His233 and Asp102) play an important role in the delivery of a fourth proton to the substrate.


  • Organizational Affiliation

    The Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, 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
290Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: queFVC_0902
EC: 1.7.1.13
UniProt
Find proteins for Q9KTK0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KTK0 
Go to UniProtKB:  Q9KTK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KTK0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download Ideal Coordinates CCD File 
K [auth B],
O [auth C]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
GUN
Query on GUN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
R [auth D]
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
I [auth B]
L [auth C]
M [auth C]
E [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
P [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
Q [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.517α = 119.25
b = 71.578β = 110.18
c = 71.511γ = 99.58
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
RESOLVEphasing
ARP/wARPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-17
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary