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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jmb.2010.09.042

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH-dependent 7-cyano-7-deazaguanine reductase
A, B, C, D
290Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Gene Names: queF
EC: 1.7.1.13
Find proteins for Q9KTK0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KTK0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
POP
Query on POP

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Download CCD File 
B, C
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GUN
Query on GUN

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Download CCD File 
A, B, C, D
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 
  • 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
HKL-3000data reduction
RESOLVEphasing
SBC-Collectdata collection
HKL-3000data collection
REFMACrefinement
MLPHAREphasing
ARP/wARPmodel building
HKL-3000phasing
HKL-3000data scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-10-17
    Type: Database references