June 2005 Molecule of the Month by David Goodsell
Keywords: beta-carotene, carotenoid-cleaving dioxygenase, retinal, vitamin A
Eat your carrots or you'll go blind! The biochemical reason for this childhood warning is that we need retinal, vitamin A, to form the pigment that absorbs light in our eyes. Unfortunately, our cells cannot make it for themselves, so we have to obtain it in our diet. We typically get our daily dose of vitamin A in two different ways. Retinal, or molecules similar to it, may be obtained directly when we eat meat. Alternatively, we can eat molecules that are easily transformed into retinal. This is where the carrots enter the story. They are full of beta-carotene, which our cells break in half to form two molecules of retinal.
The bright color of carrots and many other orange and yellow vegetables is caused by carotenoid molecules such as beta-carotene. Carotenoids are long, thin molecules with a string of carbon-carbon double bonds in a row. These bonds absorb light and give carotenoids their characteristic yellow color. Hundreds of different types have been discovered in different plants, where they color flowers, leaves, fruits, and even the roots. Carotenoids are remarkably useful, both for the plant and for the people eating the plant. In plants, carotenoids assist the chlorophyll molecules that absorb light in photosynthesis. Carotenoids also absorb excess light when it reaches dangerous levels. Our retinas contain carotenoids such as lutein that protect us from excess light that might damage our eyes. Carotenoids also are antioxidants that scavenge reactive forms of oxygen, destroying them before they damage our molecular machinery.
Carotenoids in Pieces
Carotenoids provide the starting material for construction of many useful compounds. In plants, carotenoids are broken into small pieces that act as hormones and also form small, volatile compounds with pleasing floral scents. In your cells, you break carotenoids into vitamin A, or retinal, which is used to build visual pigments and is also used as a signaling molecule to control growth and specialization of cells in our tissues. Many of these breakage reactions are performed by carotenoid oxygenases, enzymes that use a molecule of oxygen to perform the cut.
Carotenoid oxygenases trap a carotenoid molecule inside a deep pocket and break it into two pieces using oxygen. An iron ion assists in the reaction, positioning the oxygen at the proper place and activating it. The enzyme shown here, from PDB entry 2biw, is from a cyanobacterium. It breaks a variety of carotenoids at a bond at the center. Our own enzyme breaks beta-carotene in the center, forming two molecules of retinal. For more information on this family of enzymes from a genomic perspective, visit the Protein of the Month at the European Bioinformatics Institute.
Carotene and Retinal in Action
You can see carotenoids and their products at work in several structures in the PDB. Many molecules of beta-carotene may be found in the large photosystems used to capture light in photosynthesis. The example shown on the left is photosystem I from a cyanobacterium, from PDB entry 1jb0. Several beta-carotene molecules can be seen around the edge, shown here in orange. Retinal is half the size of beta-carotene, and may be found in light-sensing proteins such as rhodopsin, shown here on the right from PDB entry 1f88. The retinal, shown here in purple, is buried deep inside the protein, attached to a lysine amino acid.
Exploring the Structure
PDB entry 2biw is the first structure of a carotenoid oxygenase, revealing the mechanistic
details of this important class of enzymes. The picture shown here is a close-up of the active
site. The carotenoid, shown in orange, is held close to an iron atom, in pink. Two water
molecules, shown here with red spheres, are thought to be positioned approximately where
the oxygen will be bound when the cleavage reaction is performed. Notice that the iron atom
is gripped by four perfectly-positioned histidine amino acids.
This picture was created using RasMol. You can create similar illustrations by clicking on the accession codes here and picking one of the options under View Structure. When you go to look at this structure, notice that the PDB file contains four separate molecules of the enzyme. You will probably want to look at just one of the chains.
Additional reading about carotenoid oxygenases
G. Giuliano, S. Al-Babili and J. von Lintig (2003) Carotenoid oxygenases: cleave it or leave
it. Trends in Plant Science 8, 145-149.
G. E. Bartley and P. A. Scolnik (1995) Plant carotenoids: pigments for photoprotection, visual attraction, and human health. The Plant Cell 7, 1027-1038.
© 2015 David Goodsell & RCSB Protein Data Bank