PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Cas4 Nuclease and Bacterial Immunity
February 2014
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Stabilizing DNA Single Strands
July 2013
AlkB Homologs
August 2012
Methyl maintenance
May 2012
Follow the RNA leader
December 2011
RNA Chaperone NMB1681
July 2011
Seeing HetR
July 2011
Structure from sequence
July 2011
Added benefits
April 2011
Nitrile Reductase QueF
March 2011
Inhibiting factor
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
tRNA Isopentenyltransferase MiaA
August 2010
Mre11 Nuclease
May 2010
Seek and destroy 8-oxoguanine
May 2010
Antibiotics and Ribosome Function
March 2010
Pseudouridine Synthase TruA
November 2009
Get3 into the groove
October 2009
Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1
October 2009
Proofreading RNA
July 2009
Hda and DNA Replication
June 2009
The elusive helicase
April 2009
Poly(A) RNA recognition
January 2009
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
RNase T
July 2008
SARS Coronavirus Nonstructural Protein 1
June 2008

Research Themes DNA and RNA

Bacteriophage Lambda cII Protein

PSI-SGKB [doi:10.3942/psi_sgkb/fm_2008_10]
Featured System - October 2008
Short description: Living cells are constantly making decisions: when to eat, when to move, even when to die.

1zs4 Living cells are constantly making decisions: when to eat, when to move, even when to die. Viruses must also make decisions, but at a much simpler level. This simplicity makes them the perfect subjects for study of regulatory networks. The lambda bacteriophage has been a favorite of scientists, since it only needs to make one big decision during its life cycle. Usually, it follows a lytic life cycle: it enters cells, forces the cell to make many copies of itself, and finally bursts out of the cell, ready to infect more cells. However, if times are lean, the bacteriophage can decide to switch to a less violent approach. In the lysogenic phase, it integrates its genome into the bacterial genome, and then it is replicated each time the bacteria divides. It hitchhikes in the bacterial genome until some signal, such as DNA damage, causes it to switch back to the lytic phase and continue its campaign of destruction.

Decisions, Decisions

Several proteins together make the decision about which type of life cycle is best for the current situation. At the center of this regulatory network are the cI repressor and cro proteins. Together they form a switch, with cI repressor maintaining the lysogenic state and cro initiating the lytic state. The cII protein is the "final arbiter" of the decision, flipping this switch to the lysogenic state if the conditions warrant it. When the time is right, cII protein binds to three promoters in the bacteriophage genome, which leads to expression of the cI repressor and a DNA integrase enzyme, and inhibition of Q, a key protein in the lytic state, and the DNA excision enzyme.

Breaking Symmetry

Researchers have been studying the cII protein for decades, and have anxiously awaited a look at the structure of this interesting protein. The cII protein poses two mysteries in molecular recognition. It is a tetramer of four identical chains, but it binds to promoters with only two repeats, with the sequence TTGCNNNNNNTTGC. Also, since these two repeats are tandem repeats, and not palindromic, the protein can't be perfectly symmetrical. In collaboration with Seth Darst's laboratory at the Rockefeller University in New York, researchers at the Midwest Center for Structural Genomics have obtained the first look at how this protein recognizes its DNA promoter, solving both of these mysteries with structures of the protein alone and the protein bound to a short piece of DNA. The cII protein contains DNA-binding domains that are connected together with flexible linkers that allow them to break symmetry and find the best orientation on the two TTGC repeats. The four chains associate into two dimers, and in each dimer, only one of the chains actually contacts the DNA.

Promoter Recognition

The DNA-binding domains make specific contacts with all four base pairs in the TTGC recognition sequence, reading the arrangement of DNA atoms in the major groove. These include hydrophobic interactions with the methyl group on the thymines, and hydrogen bonds with the cytosines and guanines (some using a water molecule as intermediary). To take a closer look at this complex interaction, the JSmol tab below displays an interactive JSmol.

HutI Imidazolonepropionase

Two structures capture HutI at the beginning and the end of its reaction. This Jmol image shows a close-up of the active site and you can switch between the two structures using the buttons below. PDB entry 2q09 is bound to an analogue of the substrate. A water molecule (large turquoise sphere) is positioned over the ring in the substrate. An iron ion (brown sphere) activates the water. Two histidines and a glutamine (in green) assist in the dehydration reaction, and three histidines and an aspa


  1. Jian, D., Kim, Y., Maxwell, K.L., Beasley, S., Zhang, R., Gussin, G.N., Edwards, A. M. and Darst, S.A. (2005) Crystal structure of bacteriophage lambda cII and its DNA complex. Molecular Cell 19, 259-269.

  2. Dodd, I.B., Shearwin, K.E. and Egan, J.B. (2005) Revisited gene regulation in bacteriophage lambda. Current Opinion in Genetics and Development 15, 145-152.

  3. Oppenheim, A.B., Kobiler, O., Stavans, J., Court,D.L. and Adhya, S. (2005) Switches in bacteriophage lambda development. Annual Review of Genetics 39, 409-429.

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