Structure of glutamine synthetase

Structure of glutamine synthetase

Molecule of the Month by David S. Goodsell

Our cells are continually faced with a changing environment. Think about what you eat. Some days you might eat a lot of protein, other days you might eat a lot of carbohydrate. Sometimes you may eat nothing but chocolate. Your body must be able to respond to these different foods, producing the proper enzymes for capturing the nutrients in each. The same is doubly true for small organisms like bacteria, which do not have as many options in choosing their diet. They must eat whatever food happens to be close by, and then mobilize the enzymes needed to use it.

1fpy-twoviews

A Molecular Computer

The enzyme glutamine synthetase is a key enzyme controlling the use ofnitrogen inside cells. Glutamine, as well as being used to build proteins,delivers nitrogen atoms to enzymes that build nitrogen-richmolecules, such as DNA bases and amino acids. So, glutamine synthetase, theenzyme that builds glutamine, must be carefully controlled. When nitrogen isneeded, it must be turned on so that the cell does not starve. But when thecell has enough nitrogen, it needs to be turned off to avoid a glut.

Glutamine synthetase acts like a tiny molecular computer, monitoring theamounts of nitrogen-rich molecules. It watches levels of amino acids likeglycine, alanine, histidine and tryptophan, and levels of nucleotides like AMPand CTP. If too much of one of these molecules is made, glutamine synthetasesenses this and slows production slightly. But as levels of all of thesenucleotides and amino acids rise, together they slow glutamine synthetase moreand more. Eventually, the enzyme grinds to a halt when the supply meets thedemand.

Communication Between Many Active Sites

The glutamine synthetase molecule shown here (PDB entry 1fpy) is from bacteria. It is composed of twelve identical subunits, each of which has an active site for the production of glutamine. When performing its reaction, the active site binds to glutamate and ammonia, and also to an ATP molecule that powers the reaction. But, the active sites also bind weakly to other amino acids and nucleotides, partially blocking the action of the enzyme. All of the many sites communicate with one another, and as the concentrations of competing molecules rise, more and more of the sites are blocked, eventually shutting down the whole enzyme. The cell has a more direct approach when it wants to shut down the enzyme. At a key tyrosine next to the active site, colored yellow here and shown by the arrow, an ADP molecule can be attached to the protein, completely blocking its action.

Lack of Control

We make several versions of glutamine synthetase in our own cells. Most of our cells make a version similar to the bacterial one shown here, but with eight subunits instead of twelve. Like the bacterial enzyme, itis controlled by the nitrogen-rich compounds down the synthetic pipeline. We also make a second glutamine synthetase in our brain. There, glutamate is used as a neurotransmitter, and glutamine synthetase is used when the glutamate is recycled after a nerve impulse is delivered. In the brain, glutamine synthetase is in constant action, so a highly-regulated version is not appropriate. Instead, the alternate form is active all the time, continually performing its essential duty.

1fpy-ligands

Two Doors

Each of the twelve active sites of glutamine synthetase has two metal ions, either magnesium or manganese (shown here in purple), bound at the center of a tunnel. The substrates enter from two sides of the tunnel: ATP enters on the exposed faces on the top and bottom of the enzyme (ATP is easily seen in the upper picture on the previous page) and glutamate and ammonia squeeze through an opening between the upper ring of subunits and the lower ring. This structure, PDB entry 1fpy, contains a ADP molecule bound in the ATP site, two manganese ions (which bind tighter than magnesium, but make the enzyme slightly slower), and an inhibitor that is about the same size and shape as glutamine.

Exploring the Structure

2gls-rasmol

Glutamine synthetase is a huge enzyme. The PDB entry 2gls is a good place to start when exploring the structure. Try using a backbone diagram like the one shown here to show the interaction between the subunits. Since the regulation of glutamine synthetase relies on communication between subunits, the subunits are tied tightly together. The end of each chain threads its way up into the middle of the neighboring subunit in the opposite ring-- notice how the subunit colored red is poking up into the blue subunit.

This illustration was created with RasMol. You can create similar illustrations by clicking on the accession codes on the list of all glutamine synthetase structures in the PDB as of June 2002 (see Accession Codes, below). Choose the RasMol option under View Structure.

Further Reading about Glutamine Synthetase

David S. Eisenberg, Harindarpal S. Gill, Gaston M.U. Pfluegl and Sergio H. Rothstein (2000): Structure-function relationships of glutamine synthetases. Biochimica et Biophysica Acta 1477, pp. 122-145.

Accession Codes

List of all glutamine synthetase structures in the PDB as of June 2002
PDB ID Authors First Page Journal Name Title Vol Year
1F1H H.S.Gill, D.Eisenberg 1903 Biochemistry The Crystal Structure of Phosphinothricin in the Active Site of Glutamine Synthetase Illuminates Mechanism of Enzymatic Inhibition 40 2001
1F52 H.S.Gill, D.Eisenberg 1903 Biochemistry The Crystal Structure of Phosphinothricin in the Active Site of Glutamine Synthetase Illuminates Mechanism of Enzymatic Inhibition 40 2001
1FPY H.S.Gill, D.Eisenberg 1903 Biochemistry The Crystal Structure of Phosphinothricin in the Active Site of Glutamine Synthetase Illuminates the Mechanism of Enzymatic Inhibition 40 2001
1FRT W.P.Burmeister, A.H.Huber, P.J.Bjorkman 379 Nature Crystal structure of the complex of rat neonatal Fc receptor with Fc. 372 1994
1IC1 J.M.Casasnovas, T.Stehle, J.H.Liu, J.H.Wang, T.A.Springer 4134 Proc Natl Acad Sci U S A A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1. 95 1998
1LGR S.H.Liaw, G.Jun, D.Eisenberg 11184 Biochemistry Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium. 33 1994
2GLS M.M.Yamashita, R.J.Almassy, C.A.Janson, D.Cascio, D.Eisenberg 17681 J Biol Chem Refined atomic model of glutamine synthetase at 3.5 A resolution. 264 1989
2LGS S.H.Liaw, C.Pan, D.Eisenberg 4996 Proc Natl Acad Sci U S A Feedback inhibition of fully unadenylylated glutamine synthetase from Salmonella typhimurium by glycine, alanine, and serine. 90 1993
3FRU D.E.Vaughn, P.J.Bjorkman 63 Structure Structural basis of pH-dependent antibody binding by the neonatal Fc receptor. 6 1998