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Research Themes Cell biology


SBKB [doi:10.3942/psi_sgkb/fm_2010_12]
Featured System - December 2010
Short description: Proteins perform most of the nanoscale tasks inside of cells, but occasionally, they need help from more exotic molecules.

3emm Proteins perform most of the nanoscale tasks inside of cells, but occasionally, they need help from more exotic molecules. For instance, very small molecules like oxygen are difficult to capture, and proteins like hemoglobin use a heme to trap them. Heme is used in many other capacities as well, including the management of electrons and the capture of other gas molecules such as nitric oxide. So, when researchers at CESG discovered a new heme-containing protein in the plant Arabidopsis, they were faced with an exciting challenge: what is the heme doing?

Heme Exposed

The heme in nitrobindin (PDB entry 3emm) is unusual in that the iron atom is rather exposed to solvent. In many heme proteins, the heme is buried deep within the protein, with perfectly-placed amino acids guarding access to the iron atom. For instance, globins have a histidine on one side of the heme, which positions the iron in the proper place, and a histidine or glutamine on the other side, leaving just enough room for oxygen to bind. Nitrobindin, on the other hand, has a similar histidine coordinated directly to the iron, but the other side of the iron is free to interact with water. This has an unusual consequence: in the presence of oxygen, the iron atom is rapidly oxidized and shows only a weak interaction with oxygen.

Managing Nitric Oxide

Testing revealed, however, that the reduced form of the protein binds to nitric oxide (NO) with substantial affinity. This has posed a mystery about the function of the protein. Nitric oxide, in spite of its significant toxicity, is widely used in animal cells as a hormone, in particular, in the local control of blood flow. It plays a similar role in plant cells as part of a complex signaling network that decides what to do when cells are infected or wounded. One clue to the function of nitrobindin is provided by the similar NO-binding protein nitrophorin. Nitrophorin is made by blood-sucking insects and used to deliver NO to their victims, where it dilates the blood vessels and provides more blood for the insect. Nitrobindin may play a similar role in plants, providing a way to store NO safely until it is needed.

Another Nitrobindin

Information from structural genomics often acts like a snowball, starting with a central piece of information, then growing around that. Building on the Arabidopsis nitrobindin structure, researchers at the CESG then looked to the human genome and found a similar protein there. The protein THAP4 includes a modified zinc finger, which binds to DNA, as well as a nitrobindin-style heme-binding domain. A recent crystallographic structure of the nitrobindin portion (PDB entry 3ia8) revealed a structure very similar to the Arabidopsis nitrobindin, with a beautifully symmetrical beta barrel, a heme-binding pocket at one end and a short 310 helix at the opposite end. Click on the image below for an interactive Jmol that presents the nitrobindin structure and its interaction with the heme.

The JSmol tab below displays an interactive JSmol

Tryptophanyl-tRNA Synthetase (PDB entries 2g36 and 2dr2)

Two structures of tryptophanyl-tRNA synthetase are overlapped here. The enzyme from Thermotoga maritima was crystallized with tryptophan, and the human enzyme was crystallized with tryptophan and tRNA. Presumably, the tRNA binds similarly in the Thermotoga enzyme. Notice that the anticodon of the tRNA (colored magenta) is predicted to bind closely to the iron-sulfur cluster (colored yellow) in the Thermotoga enzyme. Use the buttons to display the two forms of the enzyme, the


  1. Bianchetti, C. M., Blouin, G. C., Bitto, E., Olson, J. S. & Phillips, G. N. Proteins 78, 917- 931 (2010).

  2. Wendehenne, D., Durner, J. & Klessig, D. F. Curr. Op. Plant Biol. 7, 449-455 (2004).

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