The CO2-fixing RuBisCO, a respectable representative of life on Earth, is my fourth structure of Christmas.
If a Martian visited Earth and was asked to report back on the most important protein in our biosphere, quite possibly it would choose RuBisCO. As enzymes go it isn’t the biggest, but it is a very big deal. It is extremely common – every single plant and photosynthetic cyanobacterium is stuffed full of it – and it performs one of the most crucial reactions for all of life: “fixing” gaseous carbon dioxide into sugars and amino acids.
RuBisCO makes all life possible. This is true directly for plants (which are autotrophs, generating their own energy), and indirectly for animals, fungi and other beasties, which ultimately depend on eating plants for energy. Yet quite astonishingly, despite the pivotal importance of its function, this is enzyme is at the bottom of the league in terms of performance.
Vital, but clunky
Evolution has found amazing solutions that allow life forms to carry out all sorts of chemical reactions quickly. Yet RuBisCO is a clunky, slow enzyme, with a bizarre and annoying side reaction involving oxygen. To make up for these peculiarities plants have to be stuffed full of this protein, and some even go to insane lengths to manage it.
Even the name RuBisCO is clunky. It’s a contraction of the full, rather long-winded name of the enzyme: ribulose-1,5-bisphosphate carboxylase/oxygenase. The curious capitalisation of the contraction has stuck for some reason, if only to plague STM copyeditors everywhere [Mary’s words, not mine!].
RuBisCO catalyses a step in the Calvin cycle, which happens in the chloroplast: a symbiotic cyanobacterium that struck a good deal with the first eukaryotic plants aeons ago.
Here’s how it works:
- Every round of the Calvin cycle adds a carbon atom to a five-carbon sugar.
- The very ‘first’ (by convention) reaction in the cycle is a critical one, catalysed by RuBisCo. In it, ribulose (a five-carbon sugar) gets converted with the addition of carbon dioxide, into two 3-carbon compounds: 3-phosphoglycerate.
- After three rounds of the cycle, six glycerate molecules have been produced. Five of these are used to regenerate three input ribuloses.
- The remaining glycerate is like the ‘carbon dividend’ of the cycle, and is used to make sugars or amino acids.
Slow but steady
Many enzymes can zip through thousands of reactions every second, but not RuBisCO. It carries out five or so carbon fixes per second – a rather stately pace.
It is a mystery why this enzyme is so slow, but it seems to be the right tool for the job. The fact that plants are stuffed full of it is a testament to its importance. It can be made to run a bit faster by providing more input material, which is why having greenhouses with higher carbon dioxide levels is good for plants.
RuBisCO is a bit needy, roping in helper proteins – called chaperones – just to get itself into the right shape. Using some elegant protein engineering, researchers have been able to improve its efficiency – but they haven’t quite beat Nature yet. Frustratingly, when the engineered RuBisCOs are put back into plants, they don’t lead to better growth.
Changing the world, one molecule at a time
But the weirdness doesn’t stop there.
RuBisCO evolved billions of years ago, before oxygen became a big player in the atmosphere. At that time, certain cyanobacteria made a breakthrough: they could capture reducing elements, needed to power the cell by splitting hydrogen atoms from water – one of the most abundant chemicals on earth. The by-product of this process is, of course, oxygen.
These cyanobacteria were tremendously successful, and one branch eventually became chloroplasts in plants. They rose as the dominant autotroph on our planet, each one pumping out molecular oxygen as they split water to capture the protons.
So this one little innovation quite literally changed the world, as gaseous oxygen is very, well, oxidising. It gave rise not only to the air that sustains animal life but a huge range of Earth-transforming reactions, such as rust in iron deposits and the creation of entirely new rock formations.
All of life had to adapt or hide from this gaseous oxygen.
Hedging its bets?
RuBisCO seems to have adapted only partly to the new world it helped create. A large proportion of its reactions swap oxygen for carbon dioxide, so instead of creating two 3-carbon molecules, it creates one 3-carbon molecule and one 2-carbon molecule. This yields no gain in carbons, and results in a loss in energy.
Some plants even seem to long for their lost world, and go through the rather bizarre process of recreating a primitive, low-oxygen world inside them. They have special structures to increase the concentration of carbon dioxide and decrease the concentration of oxygen, sometimes using plant haemoglobins (distant cousins to the proteins that carry oxygen around your blood) to sequester it.
Why hasn’t it adapted completely? Is it just ‘lazy’, or perhaps ready for calamity?
A job half done
It is still a conundrum why RuBisCO is quite such a ‘bad’ enzyme. Was its role in life just so important that it couldn’t risk evolving to be more efficient? Or is there something profoundly difficult about capturing carbon dioxide and differentiating it from oxygen? Perhaps there is something else we don’t understand about the regulation of the speed of carbon fixation?
Whatever the cause of its poor performance, humans are eager to ramp it up. If human ingenuity can ‘improve’ Nature by fixing this carbon fixer, we will have done something that could change the world, again, for the better. I’m very keen to see RuBisCO’s frustrating oxygen inefficiency tidied up, and to see what people come up with in their quest to design an efficient variant of this intriguing enzyme.
Whatever the case, we’ll have to be sure to send an update to Mars.
How they do it
Seeing structures at the EMBL Beamline
This particular RuBisCO structure – 1rbo – is one of the thousands of structures which have been determined on an EMBL Beamline, in this case the EMBL beamlines at the synchrotron DORIS on the DESY campus in Hamburg. (DORIS has gone, but EMBL now runs beamlines on the PETRAIII synchrotron on the DESY campus.)
Synchrotrons are sources of high-energy X-rays. They were originally used as machines for particle physics experiments, but biologists have also realised the potential of the X-rays produced by synchrotrons for studying the structure of molecules such as proteins.
As electrons are sent at high speed around the circular path of the synchrotron, energy in the form of X-rays is produced as a byproduct, which is emitted at a tangent to the path of the electron – much like you might lose loose change from your pockets while on a ride at the fair. These X-rays are channelled down ‘beamlines’ to where the scientist is waiting with a sample. A series of mirrors and other optical equipment focuses the powerful beam and tunes it to the wavelength, dimensions and qualities the scientist needs for his or her specific experiment.
EMBL (of which EMBL-EBI is a part) has two of its sites next door to large European synchrotrons: one in Hamburg in northern Germany, and one in Grenoble, France. EMBL uses beamlines for biological research – tapping into this source of X-rays for probing biological structures.