Secondary Structure of Integrases

Structures determined by the Macromolecular Crystallography Laboratory, Protein Structure Section at the NCI-Frederick campus. Work performed in collaboration with the Skalka Laboratory in the Institute for Cancer Research, Fox Chase Cancer Center.

---

Secondary structure refers to the way a single protein (macromolecule) folds together. The amino acid sequence, also called primary structure, determines the nature of a protein- what it does, how it interacts with other proteins, and how it folds. Since we cannot observe all the details of how a protein will fold from the sequence, solving the secondary structure (by X-ray crystallography, as shown here, or by nuclear magnetic resonance [NMR]) is important. Many sequences can fold into similar secondary structures, which is often the case for different proteins that perform similar jobs on various targets. Secondary structure also comprises the placement of specific amino acids and how they interact with metal cations, other molecules, or inhibitors.

Protein secondary structure falls into three basic categories: helix (helices), strand(s), and random coil(s). The word helix is familiar to many people from the famous term "DNA double helix". Proteins have helices as well, shown as the tight yellow and brown spirals. Strands are extended lengths of amino acids, shown as flat blue and green ribbons. One almost never refers to a single "strand" alone, because a strand is stable only when it is lying along other strands or helices. A minimum of three strands are present most of the time, with several strands together forming a "sheet". The rest of the structure is called a random coil or "loop", simply because it does not fall into the other known protein secondary structure classes (helices or strands/sheets).