PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Community-Nominated Targets
July 2015
Drug Discovery: Solving the Structure of an Anti-hypertension Drug Target
July 2015
Retrospective: 7,000 Structures Closer to Understanding Biology
July 2015
Design and Evolution: Unveiling Translocator Proteins
June 2015
Signaling with DivL
May 2015
Signaling: A Platform for Opposing Functions
May 2015
Signaling: Securing Lipid-Protein Partnership
May 2015
Dynamic DnaK
March 2015
Iron-Sulfur Cluster Biosynthesis
December 2014
Mitochondrion: Flipping for UCP2
December 2014
Mitochondrion: Setting a New TRAP1
December 2014
Power in Numbers
August 2014
Quorum Sensing: A Groovy New Component
August 2014
Quorum Sensing: E. coli Gets Involved
August 2014
iTRAQing the Ubiquitinome
July 2014
Microbiome: The Dynamics of Infection
September 2013
Protein-Nucleic Acid Interaction: A Modified SAM to Modify tRNA
July 2013
Protein-Nucleic Acid Interaction: Versatile Glutamate
July 2013
PDZ Domains
April 2013
Alpha-Catenin Connections
March 2013
Cell-Cell Interaction: A FERM Connection
March 2013
Cell-Cell Interaction: Magic Structure from Microcrystals
March 2013
Cell-Cell Interaction: Modulating Self Recognition Affinity
March 2013
Bacterial Hemophores
January 2013
Archaeal Lipids
December 2012
Membrane Proteome: Capturing Multiple Conformations
December 2012
Lethal Tendencies
October 2012
Symmetry from Asymmetry
October 2012
A signal sensing switch
September 2012
Regulatory insights
September 2012
AlkB Homologs
August 2012
Budding ensemble
August 2012
Targeting Enzyme Function with Structural Genomics
July 2012
The machines behind the spindle assembly checkpoint
June 2012
Chaperone interactions
April 2012
Pilus Assembly Protein TadZ
April 2012
Revealing the Nuclear Pore Complex
March 2012
Topping off the proteasome
March 2012
Twist to open
March 2012
Disordered Proteins
February 2012
Analyzing an allergen
January 2012
Making Lipopolysaccharide
January 2012
Pulling on loose ends
January 2012
Terminal activation
December 2011
The Perils of Protein Secretion
November 2011
Bacterial Armor
October 2011
TLR4 regulation: heads or tails?
October 2011
Ribose production on demand
September 2011
Moving some metal
August 2011
Looking for lipids
July 2011
Ribofuranosyl Binding Protein
June 2011
A molecular switch for neuronal growth
May 2011
Cell wall recycler
May 2011
Added benefits
April 2011
NMR challenges current protein hydration dogma
March 2011
Nitrile Reductase QueF
March 2011
Tip formin
March 2011
Inhibiting factor
February 2011
PASK staying active
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
December 2010
Function following form
October 2010
tRNA Isopentenyltransferase MiaA
August 2010
Importance of extension for integrin
June 2010
April 2010
Alg13 Subunit of N-Acetylglucosamine Transferase
February 2010
Hemolysin BL
January 2010
December 2009
Two-component signaling
December 2009
Network coverage
November 2009
Pseudouridine Synthase TruA
November 2009
Unusual cell division
October 2009
Toxin-antitoxin VapBC-5
September 2009
Salicylic Acid Binding Protein 2
August 2009
Proofreading RNA
July 2009
Ykul structure solves bacterial signaling puzzle
July 2009
Hda and DNA Replication
June 2009
Controlling p53
May 2009
Mitotic checkpoint control
May 2009
Ribonuclease and Ribonuclease Inhibitor
April 2009
The elusive helicase
April 2009
March 2009
High-energy storage system
February 2009
A new class of bacterial E3 ubiquitination enzymes
January 2009
Poly(A) RNA recognition
January 2009
Activating BAX
December 2008
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
New metal-binding domain
October 2008
Blocking AmtB
September 2008
September 2008
Aspartate Dehydrogenase
August 2008
RNase T
July 2008
May 2008

Research Themes Cell biology

Nitrile Reductase QueF

SBKB [doi:10.3942/psi_sgkb/fm_2011_3]
Featured System - March 2011
Short description: Nature uses exotic chemistry to build its diverse collection of molecules.

Nature uses exotic chemistry to build its diverse collection of molecules. Some of the oddest reactions are performed on transfer RNA. Most often, these changes are made by enzymes that capture a tRNA and then make modifications, adding additional groups or swapping out a few atoms for others with different properties. These chemical changes modify the interactions of tRNA with mRNA or ribosomes, making small adjustments that refine its function as the translator of genetic information.

Unique Reduction

The bacterial nitrile reductase QueF is a key enzyme in the biosynthesis of queuosine, a modified base used in the wobble anticodon position in several types of tRNA. QueF is unusual in two respects. First, it makes its modification on a free base, instead of the normal process of modifying a nucleotide that has already been built into a tRNA chain. The new group, after a few additional modifications, is then swapped onto the tRNA anticodon by another enzyme. Second, QueF performs a unique reaction, never before observed in nature, reducing a nitrile group to a primary amine.

Tools of Reduction

QueF uses several chemical tricks to perform its exotic reaction. NADPH, a carrier of hydride groups, provides the reductive power. Two molecules of NADPH are needed to perform the full reaction, which poses a potential problem: the reaction must be performed in two steps. Unfortunately, the intermediate form, created after the first NADPH has performed its half of the reduction, is reactive and would easily be destroyed by water. The enzyme solves this problem by using a cysteine amino acid to hold the intermediate, forming a covalent bond with it and protecting it from the surrounding water.

QueF Revealed

The structure of QueF, recently solved by PSI researchers at MCSG and available in PDB entry 3bp1, reveals much of this process, and leaves some mysteries. Two subunits of the enzyme form an elongated groove. In the crystal structure, two molecules of guanine were found at either end of this groove (shown here in green), and a pyrophosphate bound right in the center (red and yellow). The little loop of protein that carries the active site cysteine is disordered and cannot be seen in the structure. Presumably it folds over the top of the groove to perform the reaction when NADPH binds.

QueF in Action

To gain more insight into the reaction, PSI researchers performed computational simulations to explore the binding of NADPH and the nucleotide base that is modified. In the final model, NADPH is stretched out in the groove, and displaces one of the guanine bases observed in the crystal structure. To take a closer look at this model, the JSmol tab below displays an interactive JSmol image.

The JSmol tab below displays an interactive JSmol

A2A Adenine Receptor (PDB entries 3qak and 3eml)

Binding of adenosine shifts the structure of the receptor to the active form. Use the buttons to flip between the active agonist-bound form and the inactive antagonist-bound form and see the motion of the receptor. There is also a button to show just the adenosine portion of the agonist ligand. In each structure, the adenine portion of the molecule is colored green, and the ribose portion is colored magenta.


  1. Kim, Y. et al. High resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism. J. Mol. Biol. 404, 127-137 (2010).

  2. Iwata-Reuyl, D. An embarrassment of riches: the enzymology of RNA modification. Curr. Op. Chem. Biol. 12, 126-133 (2008).

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health