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

AlkB Homologs

SBKB [doi:10.3942/psi_sgkb/fm_2012_8]
Featured System - August 2012
Short description: Evolution is a great tinkerer, and when cells discover a useful plan for a protein, it is often pressed to service in other capacities.

Evolution is a great tinkerer, and when cells discover a useful plan for a protein, it is often pressed to service in other capacities. The DNA repair protein AlkB is a perfect example. AlkB (shown here in a complex with DNA from PDB entry 3bkz) is a bacterial protein that has the remarkable ability to repair DNA bases that have been damaged by alkylation. Many of the repair mechanisms used by cells need to clip out the damaged regions, then rebuild the entire region. AlkB, on the other hand, does a quick fix and restores the base to its proper form. With the help of an iron ion, molecular oxygen, and a small cofactor, it adds an oxygen atom to alkylated bases, forming an aldehyde that spontaneously dissociates from the DNA.

Human Homologs

Looking in human cells, researchers have found eight proteins homologous to AlkB, which are thought to have arisen through evolution from a common AlkB ancestor protein. Researchers are now revealing the structure and function of these AlkB homologs, called ABH proteins. Two of them, ABH2 and ABH3 (shown here from PDB entries 3bu0 and 2iuw) perform a similar function of repairing alkylated DNA bases, and have structures closely similar to AlkB. ABH8, on the other hand, has a quite different function, and some unusual modifications to the structure.

Targeted Function

AlkB and ABH2 are quite promiscuous, repairing a range of different types of alkylated bases in DNA and RNA. ABH8, on the other hand, has a very specific function: it modifies one base position in a transfer RNA molecule. ABH8 contains two separate enzymes: a methylase and an AlkB-type dioxygenase. Together, they build a complex modification onto uridine bases in the wobble position of the tRNA anticodon, refining its function in protein synthesis. PSI researchers at NESG have recently solved the structure of the AlkB portion of ABH8, shown here from PDB entry 3thp. The structure also includes an additional domain (shown here at the bottom) that is important for interaction with tRNA.

Comparing the Structures

AlkB and ABH8 have similar catalytic machinery, composed of an iron ion and the cofactor 2-oxoglutarate, all held in the active site by a similar protein fold. The differences are in the regions surrounding the active site. AlkB has several long, flexible loops that surround a variety of different damaged bases, performing the corrective reaction. ABH8, on the other hand, has smaller versions of these loops, which are disordered in this structure due to their flexibility when not in complex with tRNA. ABH8 also includes an additional zinc ion and the attached RRM domain, which are important for interaction with its large tRNA target. To compare the structures of these proteins, the JSmol tab below displays an interactive JSmol.

AlkB and ABH8 (PDB entries 3bkz and 3thp)

AlkB and the dioxygenase domain of ABH8 share a similar protein fold and a similar active site. In this jmol, the dioxygenase domains are in blue and the RNA-binding domain of ABH8 is in purple. A magnanese ion, which is in the position normally occupied by iron, is in magenta and a zinc ion is in cyan in ABH8. The small molecule in green is the cofactor 2-oxoglutarate. In the AlkB structure, the alkylated base is in bright red, and has flipped into position in the active site.


  1. Pastore, C., Topalidou, I., Forouhar, F., Yan, A. C., Levy, M. & Hunt, J. F. Crystal structure and RNA binding properties of the RNA Recognition Motif (RRM) and AlkB domains of human AlkB Homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification. J. Biol. Chem. 287, 2130-2143 (2012).

  2. Yang, C.-G., et al. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 452, 961-966 (2008).

  3. Sundhein, O., et al. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J. 25, 3389-3397 (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