RCSB PDB Newsletter #20: PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

No. 20
Winter 2004


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PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

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PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

The Molecule of the Month series, by David S. Goodsell, explores the functions and significance of selected biological macromolecules for a general audience. These installments are available at www.rcsb.org/pdb/molecules/molecule_list.html. A sample of the molecules featured during this past quarter are included below:

PDB ID: 2ptn
J. Walter, W. Steigemann, T.P. Singh, H. Bartunik, W. Bode, R. Huber (1982): On the disordered activation domain in trypsinogen. Chemical labelling and low-temperature crystallography. Acta Crystallogr., Sect. B 38, p. 1462.
Trypsin: Protein Cutting Machinery

October, 2003 -- Your body needs a steady supply of amino acids for use in growth and repairs. Each day, a typical adult needs something in the range of 35-90 grams of protein, depending on their weight. Quite surprisingly, a large fraction of this may come from inside. A typical North American diet may contain 70-100 grams of protein each day. But your body also secretes 20-30 grams of digestive proteins, which are themselves digested when they finish their duties. Dead intestinal cells and proteins leaking out of blood vessels are also digested and reabsorbed as amino acids, showing that our bodies are experts at recycling.

Proteins are tough, so we use an arsenal of enzymes to digest them into their component amino acids. Digestion of proteins begins in the stomach, where hydrochloric acid unfolds proteins and the enzyme pepsin begins a rough disassembly. The real work then starts in the intestines. The pancreas adds a collection of protein-cutting enzymes, with trypsin playing the central role, that chop the protein chains into pieces just a few amino acids long. Then, enzymes on the surfaces of intestinal cells and inside the cells chop them into amino acids, ready for use throughout the body.

Trypsin uses a special serine amino acid in its protein-cutting reaction, and is consequently known as a serine protease. The serine proteases are a diverse family of enzymes, all of which use similar enzymatic machinery. In digestion, trypsin, chymotrypsin and elastase work together to chop up proteins. Each has a particular taste for protein chains: trypsin (shown in PDB entry 2ptn) cuts next to lysine and arginine, chymotrypsin (shown in PDB entry 2cha) cuts next to phenylalanine and other large amino acids, and elastase likes chains with small amino acids like alanine (shown in PDB entry 3est). Trypsin-like enzymes are also found in many other places in the body. Some of these are highly specific, cleaving only a specific target protein. For instance, thrombin, presented in the Molecule of the Month in January 2002, is designed to make a specific cut in fibrinogen, creating a blood clot.

For more information about trypsin, see www.rcsb.org/pdb/molecules/pdb46_2.html..

Simian Virus 40: Steering the Cycle of Life

PDB ID: 1sva
T. Stehle, S.J. Gamblin, Y. Yan, S.C. Harrison (1996): The structure of simian virus 40 refined at 3.1 ? resolution. Structure 4, p. 165.

November, 2003 -- Simian virus 40 is an example of how simple a virus can be and still perform its deadly job. Viruses are tiny machines with a single purpose: to reproduce themselves. They enter cells and hijack their synthetic machinery, forcing them to create new viruses. SV40 does this with very little molecular machinery. It is enclosed by a spherical capsid composed of 360 copies of one protein, seen in PDB entry 1sva, and a few copies of two others. This capsid is just big enough to enclose a small circle of DNA 5,243 nucleotides long, which contains the barest minimum of information needed to get into the cell and make new viruses.

The circular SV40 genome is found in the cell as a "mini-chromosome" wound into a handful of nucleosomes. It only has enough space to encode a few functions, since it all has to fit inside the tiny capsid. It has a regulatory region that controls the entire life- cycle of the virus. It also encodes several proteins: the T-antigen (and a spliced version of it called the t-antigen) and three capsid proteins, VP1, VP2 and VP3. Only a few tiny segments are not used. Space is so limited in this genome that the capsid proteins are actually encoded with overlapping reading frames, such that the end portion of the gene for one protein also encodes for the beginning portion of the next protein. For more information on the parsimonious genome of SV40, take a look at the European Bioinformatics Institute's Protein of the Month feature at www.ebi.ac.uk/interpro/potm/archive.html.

SV40 infects primate cells, forcing its way inside and releasing its DNA circle. Once inside, it has two jobs: to replicate its DNA and to package it inside new viral capsids. Amazingly, SV40 only needs one protein, the T-antigen, to control both of these processes. Soon after the virus enters the cell, the cell's own synthetic machinery recognizes a TATA sequence at the center of the SV40 regulatory regions. The cell then creates a messenger RNA reading counterclockwise around the DNA circle. This mRNA is used to make the T-antigen protein. Then the virus really gets to work. The T-antigen binds to the SV40 circle and helps to separate the strands, making way for the cell's polymerases to copy the DNA. It also directs the reading of the DNA in the opposite direction, clockwise around the strand, to create many copies of the capsid proteins.

For more information on simian virus 40, see www.rcsb.org/pdb/molecules/pdb47_2.html.

Catabolite Activator Protein: a Second Messenger

PDB ID: 1cgp
S.C. Schultz, G.C. Shields, T.A. Steitz (1991): Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, p. 1001.

December, 2003 -- Bacteria love sugar. In particular, bacteria love glucose, which is easily digestible and quickly converted to chemical energy. When glucose is plentiful, bacteria ignore other nutrients in their environment, feasting on their favored source. But, when glucose is rare, they shift gears and mobilize the machinery needed to use other sources of energy.

Bacteria use an unusual modification of ATP, the molecule that carries chemical energy in the cell, to notify its synthetic machinery about what it is currently eating. As glucose levels drop, the cell-surface enzyme adenyl cyclase is activated. It grabs ATP molecules, clips off two phosphates, and reconnects the free end back onto the molecule, creating an odd little molecular loop through the phosphate. This product, called cyclic AMP, is released and it spreads through the cell, stimulating production of the enzymes that process other food molecules. Because of its role in delivering messages from the primary glucose sensor (adenyl cyclase) to the synthetic machinery, cyclic AMP is often known as a second messenger.

Catabolite activator protein (CAP), also known as cyclic AMP receptor protein (CRP), is activated by cyclic AMP and stimulates synthesis of the enzymes that break down non-glucose food molecules. It is composed of two identical subunits, shown in PDB entry 1cgp. When cyclic AMP binds, it changes the conformation of the protein slightly, making it perfect for binding to DNA. CAP binds to a specific DNA sequence, which is found next to the genes that are activated. When CAP binds to DNA, it coaxes RNA polymerase into place, beginning transcription.

For more information about the catabolite activator protein, see www.rcsb.org/pdb/molecules/pdb48_2.html.