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

Tryptophanyl-tRNA Synthetase

SBKB [doi:10.3942/psi_sgkb/fm_2011_2]
Featured System - February 2011
Short description: Biology is full of surprises, and they often tell us important things about ourselves.

Biology is full of surprises, and they often tell us important things about ourselves. Crystallography is no exception: often, unexpected things appear once a structure is solved. The recent structure of a bacterial tryptophanyl-tRNA synthetase, solved by researchers at JCSG, revealed two unexpected features.

Iron Strength

The biggest surprise in the structure, available in PDB entry 2g36, was the discovery of an iron-sulfur cluster. Tryptophanyl-tRNA synthetase is an elongated dimeric enzyme, with the tryptophan-adding machinery at near the center, and the tRNA-recognizing elements at the two ends. The active site is very similar to the enzymes from other organisms, but the tRNA-recognizing portion is built around four cysteines, which together trap an iron-sulfur cluster.

A Happy Accident

A second surprise occurred in the active site: the crystals include a molecule of tryptophan bound in each subunit of the enzyme. This came as a surprise, since tryptophan was not added to the mixture of molecules used to crystallize the enzyme. So, these tryptophan molecules must have hitchhiked along with the enzyme through the entire process of expression and purification, ultimately showing up in the electron density map. This is a reflection of the tight binding and specificity of the active site for tryptophan, which is essential for its function in adding the proper amino acid to its target tRNA.

Why Iron?

The presence of tryptophan in the structure is easily explained, but why is there an iron-sulfur cluster? This is the first time that an iron-sulfur cluster has been seen in aminoacyl-tRNA synthetases, but after searching through genomic sequences, a similar four-cysteine motif was found in a variety of other species. Also, given that iron-sulfur clusters are rather expensive to construct, we might guess that it's playing an important functional role. Researchers at PSI have hypothesized that the cluster may be needed to recognize the particular modifications of the tRNA, but a definitive answer will have to wait until these tRNA modifications are fully characterized.
To take a look at the Thermotoga enzyme and a model of how tRNA binds, click on the image of the iron-sulfur cluster for an interactive Jmol. To learn more about the protein or make a comment about the possible role of the iron-sulfur cluster, take a look at the page at TOPSAN.

The JSmol tab below displays an interactive JSmol

Potassium Ion Transporter TrkH (PDB entry 3pjz)

The selectivity filter of TrkH includes a precise array of oxygen atoms that mimic the water structure around a free potassium ion. In this Jmol image, the potassium ion is shown in magenta, surrounded by the eight oxygens provided by the protein peptide groups. Use the buttons to zoom out to view the entire protein, to highlight the four pore helices that point their negative ends towards the ion, and to highlight the small intramembrane loop that partially blocks the pore and may be important


  1. Han, G. W. et al. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster. Acta Cryst. F66, 1326-1334 (2010).
    Shen, N., Guo, L., Jin, Y. & Ding, J. Structure of human tryptophanyl-tRNA synthetase in complex with tRNAtrp reveals the molecular basis of tRNA recognition and specificity. Nucl. Acids Res. 34, 3246-3258 (2006).

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