Molecule of the Month: PhiX174 YES Complex

Bacteriophage phiX174 makes a small protein that kills bacterial cells.

YES complex composed of MraY (blue), phiX174 E protein (orange), and SlyD (green). The inner membrane of the bacterium is shown schematically in gray.
YES complex composed of MraY (blue), phiX174 E protein (orange), and SlyD (green). The inner membrane of the bacterium is shown schematically in gray.
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Bacteriophages are natural predators of bacteria. A bacteriophage binds to the surface of a bacterium and injects its genome, which is often composed of a single strand of DNA. This genome then directs the construction of many new copies of the bacteriophage, which burst out of the cell, killing it. Bacteriophages are everywhere in the environment, and most bacteria have many types of bacteriophages that attack them. For example, two well-studied bacteriophages, T4 and phiX174, both attack Escherichia coli bacteria.

Breaking the Sheath

Once bacteriophages have multiplied inside a cell, they face a challenge: how do they get out? Bacterial cells are often surrounded by a layer of peptidoglycan, a tough network of protein and sugar chains. So bacteriophages need proteins that corrupt this protective sheath. Bacteriophage T4 uses the enzyme lysozyme, which breaks the peptidoglycan chains. Bacteriophage phiX174, on the other hand, builds a small protein, termed protein E, that blocks the machinery that builds the peptidoglycan sheath.

Say YES to Protein E

PDB entry 8g02 reveals the mode of action of protein E. It binds to the bacterial enzyme MraY, which plays a central role in peptidoglycan synthesis. MraY attaches small precursors of peptidoglycan to a lipid carrier. The lipid makes it easy for other proteins to flip the precursor to the outside of the cell and attach it to growing peptidoglycan chains. Protein E blocks this process by binding to MraY and covering up the active site. Protein E also recruits a second protein, the chaperone protein SlyD, further occluding the active site of MraY. The whole complex, including MraY, protein E, and SlyD, has been termed the YES complex.

Phage Therapy

Since phages kill bacteria, they can be useful for treating infections. Phage therapy has been used for over a century, starting with treatment of dysentery with phages in 1919. It fell out of use in western medicine after the discovery of penicillin and other antibiotic drugs. Antibiotics have major advantages: they are easy to administer and they often target a wide range of bacteria. However, the recent emergence of antibiotic-resistant strains of bacteria has rekindled interest in phage therapy, which can provide an effective alternative for infections where no effective antibiotic drugs are available.

Tube-forming domain of phiX174 H protein.
Tube-forming domain of phiX174 H protein.
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DNA Injection

Bacterial cell walls also cause problems during the first steps of bacteriophage infection. Many bacteriophages, such as T4, have elaborate tails that bind to the surface of bacteria and inject their DNA through the wall. PhiX174 takes a simpler approach. It encodes a protein that assembles into a tube at the last minute, building a pathway through the cell wall just large enough for the DNA. PDB ID 4jpp includes the tube-forming portion of the protein.

Exploring the Structure

YES Complex and Antibiotic

Many antibiotics attack the bacterial enzymes that build the peptidoglycan sheath. For example, penicillin blocks the enzymes that connect precursors together to form the network. The natural antibiotic muraymycin D2 binds to MraY (PDB ID 5ckr), blocking the active site similarly to phiX174 E protein. To explore these two structures in more detail, click on the JSmol tab for an interactive view.

Topics for Further Discussion

  1. You can learn more about bacteriophages and other viruses in Exploring the Structural Biology of Viruses.
  2. You can explore the biology and structures of antibiotic resistance in resources at PDB-101.


  1. 8g02: Orta, A.K., Riera, N., Li, Y.E., Tanaka, S., Yun, H.G., Klaic, L., Clemons Jr., W.M. (2023) The mechanism of the phage-encoded protein antibiotic from Phi X174. Science 381: eadg9091-eadg9091
  2. Strathdee, S.A., Hatfull, G.F., Mutalik, V.K., Schooley, R.T. (2023) Phage therapy: From biological mechanisms to future directions. Cell 186, 17-31
  3. 5ckr: Chung, B.C., Mashalidis, E.H., Tanino, T., Kim, M., Matsuda, A., Hong, J., Ichikawa, S., Lee, S.Y. (2016) Structural insights into inhibition of lipid I production in bacterial cell wall synthesis. Nature 533: 557-560
  4. 4jpp: Sun, L., Young, L.N., Zhang, X., Boudko, S.P., Fokine, A., Zbornik, E., Roznowski, A.P., Molineux, I.J., Rossmann, M.G., Fane, B.A. (2014) Icosahedral bacteriophage Phi X174 forms a tail for DNA transport during infection. Nature 505: 431-435

April 2024, David Goodsell
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More